Re: [Freesurfer] problem of regist MNI .nifti volume to fsaverage space

[Thomas Yeo]

Hi Amy,

Have you tried the "--mni152reg" flag instead of "--reg
/usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat". Is the
attached picture from your original command or mni152reg flag?

p.s. Can you please reply all to the freesurfer list?

Cheers,
Thomas

On Mon, Mar 2, 2015 at 6:54 PM, Amy Lin  wrote:
> Hello Thomas, thanks for the tips but the result still look strange. please
> help me to take a look as the attached picture. Another question is how to
> adjust the color bar and assign by my define look up table.
>
> This is my command:
>
> amy@ubuntu:~/Downloads$ mri_vol2surf --mov my_MNI_ROIs.nii --reg
> /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --hemi lh
> --inflated --o lh.ROIs.mgh
> srcvol = my_MNI_ROIs.nii
> srcreg = /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat
> srcregold = 0
> srcwarp unspecified
> surf = inflated
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Reading surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 18019
> Writing to lh.ROIs.mgh
> Dim: 163842 1 1
> amy@ubuntu:~/Downloads$ tksurfer fsaverage lh inflated -overlay lh.ROIs.mgh
> subject is fsaverage
> hemiis lh
> surface is inflated
> surfer: current subjects dir: /usr/local/freesurfer/subjects
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /home/amy/Downloads
> checking for nofix files in 'inflated'
> Reading image info (/usr/local/freesurfer/subjects/fsaverage)
> Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
> surfer: Reading header info from
> /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
> surfer: vertices=163842, faces=327680
> tkmedit: Trying to open lh.ROIs.dat
> surfer: Interpreting overlay volume lh.ROIs.mgh as encoded scalar volume.
> surfer: curvature read: min=-0.673989 max=0.540227
> surfer: single buffered window
> surfer: tkoInitWindow(fsaverage)
> surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl
> Reading /usr/local/freesurfer/tktools/tkm_common.tcl
> Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/tktools/tkUtils.tcl
> Successfully parsed tksurfer.tcl
> reading white matter vertex locations...
>
> On Mon, Mar 2, 2015 at 1:15 AM, Thomas Yeo  wrote:
>>
>> Hi Amy,
>>
>> What exactly is the command you use?
>>
>> The command should be something like for the right hemisphere:
>> mri_vol2surf --mov youROIs.nii.gz --mni152reg --hemi rh --surf
>> inflated --o rh.ROIs.mgh
>>
>> You need to repeat for the left hemisphere. I am cc-ing the freesurfer
>> list to keep our conversation on the list.
>>
>> Cheers,
>> Thomas
>>
>>
>> On Mon, Mar 2, 2015 at 3:38 AM, Amy Lin  wrote:
>> > hi, thanks for reply the email. i use command mri_vol2surf try to map my
>> > define ROI (.nii) to inflated brain. the command work but not so good in
>> > my
>> > case.  My question is how to generate the inflated brain similar as the
>> > attached picture with my define ROIs.
>> >
>> > Amy
>> >
>> > On Feb 28, 2015 1:02 AM, "Thomas Yeo"  wrote:
>> >>
>> >> Hi Amy,
>> >>
>> >> I am confused. Are you trying to run recon-all? From what you said,
>> >> you have some ROIs in MNI space, which you want to map to fsaverage
>> >> space?
>> >>
>> >> p.s. Can you post your question to the freesurfer list instead of
>> >> directly emailing me?
>> >>
>> >> Cheers,
>> >> Thomas
>> >>
>> >> On Sat, Feb 28, 2015 at 12:02 AM, Amy Lin  wrote:
>> >> > Hello Thomas,
>> >> >
>> >> > I have one quick question for the registration issue from the MNI
>> >> > volume
>> >> > to
>> >> > the freesurfer fsaverage sphere and inflated space. I can not
>> >> > generate
>> >> > the
>> >> > correct .gcs or the .annot file from the my MNI .nifti file .
>> >> >
>> >> > -MNI volume contain several ROIs (see the attached file and the
>> >> > follows
>> >> > link
>> >> > (https://www.dropbox.com/s/f84tm4rwuovyr8p/my_MNI_ROIs.nii?dl=0)
>> >> >
>> >> > Do you have any tips for this?
>> >> > Thanks for the time.
>> >> >
>> >> > Best,
>> >> > Amy Lin
>> >> >
>> >> >
>
>
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Re: [Freesurfer] problem of regist MNI .nifti volume to fsaverage space

[Thomas Yeo]

Hi Amy,

Good point. You can first use mri_vol2vol to upsample to 1mm:

mri_vol2vol --mov yourROIs.nii --targ
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o
yourROIs_1mm.nii --interp nearest

then

mri_vol2surf --mov yourROIs_1mm.nii --mni152reg --hemi rh --surf white
--o rh.ROIs.mgh

You can then visualize with freeview:

freeview -f 
$FREESURFER_HOME/subjects/fsaverage/surf/rh.inflated:overlay=rh.ROIs.mgh

By default it uses a heatmap, so you have to adjust the overlay accordingly.

Cheers,
Thomas

On Mon, Mar 2, 2015 at 7:39 PM, Amy Lin  wrote:
> hi, of course. The result look strange too. Please see the attached file
> with -mni152reg command and this transformation matrix is not for the 2mm
> resolution image. lets me know if you have any other suggestion. thanks.
>
> Amy
>
>
> On Mon, Mar 2, 2015 at 12:26 PM, Thomas Yeo  wrote:
>>
>> Hi Amy,
>>
>> Have you tried the "--mni152reg" flag instead of "--reg
>> /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat". Is the
>> attached picture from your original command or mni152reg flag?
>>
>> p.s. Can you please reply all to the freesurfer list?
>>
>> Cheers,
>> Thomas
>>
>> On Mon, Mar 2, 2015 at 6:54 PM, Amy Lin  wrote:
>> > Hello Thomas, thanks for the tips but the result still look strange.
>> > please
>> > help me to take a look as the attached picture. Another question is how
>> > to
>> > adjust the color bar and assign by my define look up table.
>> >
>> > This is my command:
>> >
>> > amy@ubuntu:~/Downloads$ mri_vol2surf --mov my_MNI_ROIs.nii --reg
>> > /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --hemi lh
>> > --inflated --o lh.ROIs.mgh
>> > srcvol = my_MNI_ROIs.nii
>> > srcreg = /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat
>> > srcregold = 0
>> > srcwarp unspecified
>> > surf = inflated
>> > hemi = lh
>> > reshape = 0
>> > interp = nearest
>> > float2int = round
>> > GetProjMax = 0
>> > INFO: float2int code = 0
>> > Done loading volume
>> > Reading surface
>> > /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated
>> > Done reading source surface
>> > Mapping Source Volume onto Source Subject Surface
>> >  1 0 0 0
>> > using old
>> > Done mapping volume to surface
>> > Number of source voxels hit = 18019
>> > Writing to lh.ROIs.mgh
>> > Dim: 163842 1 1
>> > amy@ubuntu:~/Downloads$ tksurfer fsaverage lh inflated -overlay
>> > lh.ROIs.mgh
>> > subject is fsaverage
>> > hemiis lh
>> > surface is inflated
>> > surfer: current subjects dir: /usr/local/freesurfer/subjects
>> > surfer: not in "scripts" dir ==> using cwd for session root
>> > surfer: session root data dir ($session) set to:
>> > surfer: /home/amy/Downloads
>> > checking for nofix files in 'inflated'
>> > Reading image info (/usr/local/freesurfer/subjects/fsaverage)
>> > Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
>> > surfer: Reading header info from
>> > /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
>> > surfer: vertices=163842, faces=327680
>> > tkmedit: Trying to open lh.ROIs.dat
>> > surfer: Interpreting overlay volume lh.ROIs.mgh as encoded scalar
>> > volume.
>> > surfer: curvature read: min=-0.673989 max=0.540227
>> > surfer: single buffered window
>> > surfer: tkoInitWindow(fsaverage)
>> > surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl
>> > Reading /usr/local/freesurfer/tktools/tkm_common.tcl
>> > Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
>> > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
>> > Reading /usr/local/freesurfer/tktools/tkUtils.tcl
>> > Successfully parsed tksurfer.tcl
>> > reading white matter vertex locations...
>> >
>> > On Mon, Mar 2, 2015 at 1:15 AM, Thomas Yeo 
>> > wrote:
>> >>
>> >> Hi Amy,
>> >>
>> >> What exactly is the command you use?
>> >>
>> >> The command should be something like for the right hemisphere:
>> >> mri_vol2surf --mov youROIs.nii.gz --mni152reg --hemi rh --surf
>> >> inflated --o rh.ROIs.mgh
>> >>
>> >> You need to repeat for the left hemisphere. I am cc-ing the freesurfer
>> >> list to keep our conversation on the list.
>> >>
>> >> Cheers,
>>

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Yu-Chieh,

I am cc-ing the freesurfer list who may help you with your issues.

Can you explain what exactly you are trying do? The parcellation is
released in different resolutions including fsaverage5. Why can't you
just use the fsaverage5 parcellation?

Cheers,
Thomas

On Fri, May 1, 2015 at 6:14 PM, 陳昱潔  wrote:
> Dear professor Yeo :
>
>My name is Yu-chieh Chen , I am a graduated student from National Taiwan
> University of medical school, and my supervisor is professor Susan Shur-Fen
> Gau from department of psychiatry, National Taiwan University Hospital &
> College of Medicine. We are very interesting about your paper published in
> 2011 which using resting MRI to separate brain regions to functional
> networks. We'd like to use your percellation to re-separate the brain
> regions based on your released data in Freesurfer(
> http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). And use
> these volume of brain regions for our study, however, there comes the
> problem that we assumed that we can change the fsaverage into fsaverage5,
> thus we may get the new volume of the parcellation_Yeo. But it is not work.
> So I send this email for help. Last , I am very appreciate your kindness and
> very sorry for my inappropriate and rough.
> Thank you very much for read this email and sorry for occupied your time.
>
> Best wishes,
> Yu-chieh Chen
>

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Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

Please cc the freesurfer list when you reply because there might be
other people more qualified to answer your question.

Based on what you are saying, I think you can first use mri_surf2surf
(with the "sval-annot" flag) to transform the 2011 functional networks
.annot file from fsaverage space to the subject's native surface
space. Type "mri_surf2surf --help" to see examples.

You can then use mris_anatomical_stats to compute thickness statistics.

Cheers,
Thomas

On Tue, May 5, 2015 at 3:21 PM, 陳昱潔  wrote:
> Dear Pro. Yeo:
>
>  Very appreciate for your reply !
>
> We are trying to use your definition of the functional network regions to
> re-parcellate our images
> and get the regions of volume or cortical thickness for our study interest
> of structural network.
> However, we did not want to re-run the first recon-all again due to it's
> spending to much time.
> And we are still can't find the way to solve this problem.
> Thank you very much for helping us!
>
> Best wishes,
> Annie Chen
>
> 2015-05-02 8:25 GMT+08:00 Thomas Yeo :
>>
>> Hi Yu-Chieh,
>>
>> I am cc-ing the freesurfer list who may help you with your issues.
>>
>> Can you explain what exactly you are trying do? The parcellation is
>> released in different resolutions including fsaverage5. Why can't you
>> just use the fsaverage5 parcellation?
>>
>> Cheers,
>> Thomas
>>
>> On Fri, May 1, 2015 at 6:14 PM, 陳昱潔  wrote:
>> > Dear professor Yeo :
>> >
>> >My name is Yu-chieh Chen , I am a graduated student from National
>> > Taiwan
>> > University of medical school, and my supervisor is professor Susan
>> > Shur-Fen
>> > Gau from department of psychiatry, National Taiwan University Hospital &
>> > College of Medicine. We are very interesting about your paper published
>> > in
>> > 2011 which using resting MRI to separate brain regions to functional
>> > networks. We'd like to use your percellation to re-separate the brain
>> > regions based on your released data in Freesurfer(
>> > http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). And
>> > use
>> > these volume of brain regions for our study, however, there comes the
>> > problem that we assumed that we can change the fsaverage into
>> > fsaverage5,
>> > thus we may get the new volume of the parcellation_Yeo. But it is not
>> > work.
>> > So I send this email for help. Last , I am very appreciate your kindness
>> > and
>> > very sorry for my inappropriate and rough.
>> > Thank you very much for read this email and sorry for occupied your
>> > time.
>> >
>> > Best wishes,
>> > Yu-chieh Chen
>> >
>
>

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

mri_surf2surf is complaining that it cannot write out the annotation.

Just to clarify, is your subject called test_run_allindex? In other
words, is the variable s equal to test_run_allindex?

Does the directory "/home/annie/test_run_allindex/label/" exist? If
not, then you first need to create the directory first, and then
mri_surf2surf can write the resulting annotation file into the
directory.

Cheers,
Thomas

On Tue, May 12, 2015 at 5:46 PM, 陳昱潔  wrote:
> Hi Professor Yeo :
>
>We tried the code
>>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>>> --sval-annot
>>>
>>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
> However there came an error of "could not write annot file
> /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot
> No such file or directory"
> And we checked our individual subject's label there isn't
> lh.Yeo2011_7Networks_N1000.annot
> Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our
> subjects/label first?
> What can we do ?
> Thank you very much!
>
> Best wishes,
> Annie
>
>
> 2015-05-05 8:36 GMT-04:00 Thomas Yeo :
>
>> Hi Annie,
>>
>> Please cc the freesurfer list when you reply because there might be
>> other people more qualified to answer your question.
>>
>> Based on what you are saying, I think you can first use mri_surf2surf
>> (with the "sval-annot" flag) to transform the 2011 functional networks
>> .annot file from fsaverage space to the subject's native surface
>> space. Type "mri_surf2surf --help" to see examples.
>>
>> You can then use mris_anatomical_stats to compute thickness statistics.
>>
>> Cheers,
>> Thomas
>>
>> On Tue, May 5, 2015 at 3:21 PM, 陳昱潔  wrote:
>> > Dear Pro. Yeo:
>> >
>> >  Very appreciate for your reply !
>> >
>> > We are trying to use your definition of the functional network regions
>> > to
>> > re-parcellate our images
>> > and get the regions of volume or cortical thickness for our study
>> > interest
>> > of structural network.
>> > However, we did not want to re-run the first recon-all again due to it's
>> > spending to much time.
>> > And we are still can't find the way to solve this problem.
>> > Thank you very much for helping us!
>> >
>> > Best wishes,
>> > Annie Chen
>> >
>> > 2015-05-02 8:25 GMT+08:00 Thomas Yeo :
>> >>
>> >> Hi Yu-Chieh,
>> >>
>> >> I am cc-ing the freesurfer list who may help you with your issues.
>> >>
>> >> Can you explain what exactly you are trying do? The parcellation is
>> >> released in different resolutions including fsaverage5. Why can't you
>> >> just use the fsaverage5 parcellation?
>> >>
>> >> Cheers,
>> >> Thomas
>> >>
>> >> On Fri, May 1, 2015 at 6:14 PM, 陳昱潔  wrote:
>> >> > Dear professor Yeo :
>> >> >
>> >> >My name is Yu-chieh Chen , I am a graduated student from National
>> >> > Taiwan
>> >> > University of medical school, and my supervisor is professor Susan
>> >> > Shur-Fen
>> >> > Gau from department of psychiatry, National Taiwan University
>> >> > Hospital &
>> >> > College of Medicine. We are very interesting about your paper
>> >> > published
>> >> > in
>> >> > 2011 which using resting MRI to separate brain regions to functional
>> >> > networks. We'd like to use your percellation to re-separate the brain
>> >> > regions based on your released data in Freesurfer(
>> >> > http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
>> >> > And
>> >> > use
>> >> > these volume of brain regions for our study, however, there comes the
>> >> > problem that we assumed that we can change the fsaverage into
>> >> > fsaverage5,
>> >> > thus we may get the new volume of the parcellation_Yeo. But it is not
>> >> > work.
>> >> > So I send this email for help. Last , I am very appreciate your
>> >> > kindness
>> >> > and
>> >> > very sorry for my inappropriate and rough.
>> >> > Thank you very much for read this email and sorry for occupied your
>> >> > time.
>> >> >
>> >> > Best wishes,
>> >> > Yu-chieh Chen
>> >> >
>> >
>> >
>
>

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

I assume this means 5202 is your subject ID? Maybe you should check if
/home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
exist?

If so, you can run mris_anatomical_stats to generate statistics for
the parcellation.

Cheers,
Thomas

On Tue, May 12, 2015 at 6:29 PM, 陳昱潔  wrote:
> Hi Professor Yeo :
> After I rechecked the directory and run again mri_surf2surf
> I got the result:
> "Saving target data
> Converting to target annot
> Saving to target annot
> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot"
> The file of 5202/label didn't come out with lh.Yeo2011_7Networks_N1000.annot
> But it seems succeed, right?
> How can I get the stat of this parcellation ?
>
> Thank you very much!
>
> Best wishes,
> Annie
>
> 2015-05-12 6:06 GMT-04:00 Thomas Yeo :
>
>> Hi Annie,
>>
>> mri_surf2surf is complaining that it cannot write out the annotation.
>>
>> Just to clarify, is your subject called test_run_allindex? In other
>> words, is the variable s equal to test_run_allindex?
>>
>> Does the directory "/home/annie/test_run_allindex/label/" exist? If
>> not, then you first need to create the directory first, and then
>> mri_surf2surf can write the resulting annotation file into the
>> directory.
>>
>> Cheers,
>> Thomas
>>
>> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔  wrote:
>> > Hi Professor Yeo :
>> >
>> >We tried the code
>> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>> >>> --sval-annot
>> >>>
>> >>>
>> >>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
>> > However there came an error of "could not write annot file
>> > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot
>> > No such file or directory"
>> > And we checked our individual subject's label there isn't
>> > lh.Yeo2011_7Networks_N1000.annot
>> > Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our
>> > subjects/label first?
>> > What can we do ?
>> > Thank you very much!
>> >
>> > Best wishes,
>> > Annie
>> >
>> >
>> > 2015-05-05 8:36 GMT-04:00 Thomas Yeo :
>> >
>> >> Hi Annie,
>> >>
>> >> Please cc the freesurfer list when you reply because there might be
>> >> other people more qualified to answer your question.
>> >>
>> >> Based on what you are saying, I think you can first use mri_surf2surf
>> >> (with the "sval-annot" flag) to transform the 2011 functional networks
>> >> .annot file from fsaverage space to the subject's native surface
>> >> space. Type "mri_surf2surf --help" to see examples.
>> >>
>> >> You can then use mris_anatomical_stats to compute thickness statistics.
>> >>
>> >> Cheers,
>> >> Thomas
>> >>
>> >> On Tue, May 5, 2015 at 3:21 PM, 陳昱潔  wrote:
>> >> > Dear Pro. Yeo:
>> >> >
>> >> >  Very appreciate for your reply !
>> >> >
>> >> > We are trying to use your definition of the functional network
>> >> > regions
>> >> > to
>> >> > re-parcellate our images
>> >> > and get the regions of volume or cortical thickness for our study
>> >> > interest
>> >> > of structural network.
>> >> > However, we did not want to re-run the first recon-all again due to
>> >> > it's
>> >> > spending to much time.
>> >> > And we are still can't find the way to solve this problem.
>> >> > Thank you very much for helping us!
>> >> >
>> >> > Best wishes,
>> >> > Annie Chen
>> >> >
>> >> > 2015-05-02 8:25 GMT+08:00 Thomas Yeo :
>> >> >>
>> >> >> Hi Yu-Chieh,
>> >> >>
>> >> >> I am cc-ing the freesurfer list who may help you with your issues.
>> >> >>
>> >> >> Can you explain what exactly you are trying do? The parcellation is
>> >> >> released in different resolutions including fsaverage5. Why can't
>> >> >> you
>> >> >> just use the fsaverage5 parcellation?
>> >> >>
>> &

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

I have previously extracted individual regions from the 7 and 17
networks. You can download them here
(https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0).
Please see the README in the folder for more explanations. There
should be a precuneus DMN region.

The 17 networks consist of 114 regions that have been previously published:

1) Krienen et al., Reconfigurable state-dependent functional coupling
modes cluster around a core functional architecture. Philosophical
Transactions of the Royal Society B, 369:20130526, 2014

2) Yeo et al., Functional connectivity during rested wakefulness
predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
2015

Hope this helps.

Cheers,
Thomas

On Thu, May 14, 2015 at 3:08 PM, 陳昱潔  wrote:
> Hello Dr. Yeo,
>
> Thank you for your previous help and reply. We've worked out the way to
> switch the resolution of parcellation and successfully extracted the
> anatomical information using your mask derived from iFC work.
>
> However, we came across a new problem to apply the cortical mask and need
> your kind help again. We aim to conduct a seed-based analysis to investigate
> structural covariance based on the network defined by iFC, and find your
> work of cortical parcellation conceptually perfectly suit our research
> question. Based on the current approach, however, it seemed that we could
> only extract the anatomical information from the whole well-defined network,
> but not the specific hub within the network (e.g., the anatomical
> information of the precuneus from the DMN). We wonder if you have any
> suggestion to resolve our problem, ie, to be specific, is there any way to
> only extract the discrete hub information rather than the whole network?
>
> We really appreciate your generous help. Thank you very much.
>
> p.s. This email would also forward to my senior colleague, Dr. Hsiang-Yuan
> Lin, who is a child and adolescent psychiatrist doing imaging research in
> Taiwan.
>
>
> 2015-05-13 19:15 GMT+08:00 陳昱潔 :
>>
>> Hi Professor Yeo :
>>
>> Thank you for helping us so much!
>> After mris_anatomical_stat I tried aparcstats2table to extract the table.
>> But I failed with generating the table.
>>
>>
>> Best wishes,
>> Annie
>>
>> 2015-05-12 8:29 GMT-04:00 Thomas Yeo :
>>
>>> Hi Annie,
>>>
>>> I assume this means 5202 is your subject ID? Maybe you should check if
>>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
>>> exist?
>>>
>>> If so, you can run mris_anatomical_stats to generate statistics for
>>> the parcellation.
>>>
>>> Cheers,
>>> Thomas
>>>
>>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔  wrote:
>>> > Hi Professor Yeo :
>>> > After I rechecked the directory and run again mri_surf2surf
>>> > I got the result:
>>> > "Saving target data
>>> > Converting to target annot
>>> > Saving to target annot
>>> >
>>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot"
>>> > The file of 5202/label didn't come out with
>>> > lh.Yeo2011_7Networks_N1000.annot
>>> > But it seems succeed, right?
>>> > How can I get the stat of this parcellation ?
>>> >
>>> > Thank you very much!
>>> >
>>> > Best wishes,
>>> > Annie
>>> >
>>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo :
>>> >
>>> >> Hi Annie,
>>> >>
>>> >> mri_surf2surf is complaining that it cannot write out the annotation.
>>> >>
>>> >> Just to clarify, is your subject called test_run_allindex? In other
>>> >> words, is the variable s equal to test_run_allindex?
>>> >>
>>> >> Does the directory "/home/annie/test_run_allindex/label/" exist? If
>>> >> not, then you first need to create the directory first, and then
>>> >> mri_surf2surf can write the resulting annotation file into the
>>> >> directory.
>>> >>
>>> >> Cheers,
>>> >> Thomas
>>> >>
>>> >> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔  wrote:
>>> >> > Hi Professor Yeo :
>>> >> >
>>> >> >We tried the code
>>> >> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>>> >> >>> --sval-annot
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

Can you tell us the exact mri_surf2surf command you use?

Cheers,
Thomas

On Fri, May 15, 2015 at 5:24 PM, 陳昱潔  wrote:
> Hi Dr. Yeo,
>
> Thank you very much for your help! It is the exactly we need!
> Only a little question that when we ran mris_surf2surf
> Something seems wrong , but I can't figure out.
> annot file:
> /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 152420 i=00A4F8DC,
> in_array_size=10242
> annot file:
> /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 152421 i=00A4F8DC,
> in_array_size=10242
> annot file:
> /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 152422 i=00010101,
> in_array_size=10242
> annot file:
> /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot\
> reading colortable from annotation file...
> colortable with 18 entries read (originally MyColorLUT)
> Reading target surface reg
> /home/annie/test_run_allindex/5204/surf/lh.sphere.reg
> Done
> Mapping Source Volume onto Source Subject Surface
> surf2surf_nnfr: building source hash (res=16).
> Surf2Surf: Forward Loop (160564)
>
> Surf2Surf: Dividing by number of hits (160564)
> INFO: nSrcLost = 0
> nTrg121 = 160564, nTrgMulti = 0, MnTrgMultiHits = 0
> nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits =
> 15.677
> Saving target data
> Converting to target annot
> Saving to target annot
> /home/annie/test_run_allindex/5204/label/lh.Yeo2011_17Networks_N1000.annot
>
>
> Sorry for giving such long code. But it seems the vertex number didn't
> match.
> Or just something goes wrong while I proceed.
>
> Best,
> Annie
>
> 2015-05-14 4:54 GMT-04:00 Thomas Yeo :
>
>> Hi Annie,
>>
>> I have previously extracted individual regions from the 7 and 17
>> networks. You can download them here
>>
>> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0).
>> Please see the README in the folder for more explanations. There
>> should be a precuneus DMN region.
>>
>> The 17 networks consist of 114 regions that have been previously
>> published:
>>
>> 1) Krienen et al., Reconfigurable state-dependent functional coupling
>> modes cluster around a core functional architecture. Philosophical
>> Transactions of the Royal Society B, 369:20130526, 2014
>>
>> 2) Yeo et al., Functional connectivity during rested wakefulness
>> predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
>> 2015
>>
>> Hope this helps.
>>
>> Cheers,
>> Thomas
>>
>> On Thu, May 14, 2015 at 3:08 PM, 陳昱潔  wrote:
>> > Hello Dr. Yeo,
>> >
>> > Thank you for your previous help and reply. We've worked out the way to
>> > switch the resolution of parcellation and successfully extracted the
>> > anatomical information using your mask derived from iFC work.
>> >
>> > However, we came across a new problem to apply the cortical mask and
>> > need
>> > your kind help again. We aim to conduct a seed-based analysis to
>> > investigate
>> > structural covariance based on the network defined by iFC, and find your
>> > work of cortical parcellation conceptually perfectly suit our research
>> > question. Based on the current approach, however, it seemed that we
>> > could
>> > only extract the anatomical information from the whole well-defined
>> > network,
>> > but not the specific hub within the network (e.g., the anatomical
>> > information of the precuneus from the DMN). We wonder if you have any
>> > suggestion to resolve our problem, ie, to be specific, is there any way
>> > to
>> > only extract the discrete hub information rather than the whole network?
>> >
>> > We really appreciate your generous help. Thank you very much.
>> >
>> > p.s. This email would also forward to my senior colleague, Dr.
>> > Hsiang-Yuan
>> > Lin, who is a child and adolescent psychiatrist doing imaging research
>> > in
>> > Taiwan.
>> >
>> >
>> > 2015-05-13 19:15 GMT+08:00 陳昱潔 :
>> >>
>> >> Hi Professor Yeo :
>> >>
>> >> Thank you for helping us so much!
>> >> After mris_anatomical_stat I tried aparcstats2table to extract the
>> >> table.
>> >> But I faile

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

I am a little unsure why this might happen. Did you inspect if
$SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot is correct?

Cheers,
Thomas

On Mon, May 18, 2015 at 1:52 PM, 陳昱潔  wrote:
> Hi Dr. Yeo :
>
> Thank you very much for helping us a lot!
> I ran the command this below:
> mri_surf2surf --srcsubject fsaverage5 --trgsubject 5204 --hemi lh \
>--sval-annot
> $SUBJECTS_DIR/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot \
>--tval   $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot
> and after I ran this command:
> mris_anatomical_stats -a
> 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot  -b 5202 rh
> All turned out
> MRISreadAnnotationIntoArray: vertex index out of range: 892219914
> i=352E320A, in_array_size=153173
> annot file:
> 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 892219914
> i=352E320A, in_array_size=153173
> annot file:
> 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 892219914
> i=352E320A, in_array_size=153173
> annot file:
> 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 892219914
> i=352E320A, in_array_size=153173
> annot file:
> 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
> MRISreadAnnotationIntoArray: vertex index out of range: 892219914
> i=352E320A, in_array_size=153173
>
> Best wishes,
> Annie
>
> 2015-05-15 8:15 GMT-04:00 Thomas Yeo :
>
>> Hi Annie,
>>
>> Can you tell us the exact mri_surf2surf command you use?
>>
>> Cheers,
>> Thomas
>>
>> On Fri, May 15, 2015 at 5:24 PM, 陳昱潔  wrote:
>> > Hi Dr. Yeo,
>> >
>> > Thank you very much for your help! It is the exactly we need!
>> > Only a little question that when we ran mris_surf2surf
>> > Something seems wrong , but I can't figure out.
>> > annot file:
>> >
>> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 152420
>> > i=00A4F8DC,
>> > in_array_size=10242
>> > annot file:
>> >
>> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 152421
>> > i=00A4F8DC,
>> > in_array_size=10242
>> > annot file:
>> >
>> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 152422
>> > i=00010101,
>> > in_array_size=10242
>> > annot file:
>> >
>> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot\
>> > reading colortable from annotation file...
>> > colortable with 18 entries read (originally MyColorLUT)
>> > Reading target surface reg
>> > /home/annie/test_run_allindex/5204/surf/lh.sphere.reg
>> > Done
>> > Mapping Source Volume onto Source Subject Surface
>> > surf2surf_nnfr: building source hash (res=16).
>> > Surf2Surf: Forward Loop (160564)
>> >
>> > Surf2Surf: Dividing by number of hits (160564)
>> > INFO: nSrcLost = 0
>> > nTrg121 = 160564, nTrgMulti =     0, MnTrgMultiHits = 0
>> > nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits =
>> > 15.677
>> > Saving target data
>> > Converting to target annot
>> > Saving to target annot
>> >
>> > /home/annie/test_run_allindex/5204/label/lh.Yeo2011_17Networks_N1000.annot
>> >
>> >
>> > Sorry for giving such long code. But it seems the vertex number didn't
>> > match.
>> > Or just something goes wrong while I proceed.
>> >
>> > Best,
>> > Annie
>> >
>> > 2015-05-14 4:54 GMT-04:00 Thomas Yeo :
>> >
>> >> Hi Annie,
>> >>
>> >> I have previously extracted individual regions from the 7 and 17
>> >> networks. You can download them here
>> >>
>> >>
>> >> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0).
>> >> Please see the README in the folder for more explanations. There
>> >> should be a precuneus DMN region.
>> >>
>> >> The 17 networks consist of 114 regions that have been previously
>> >> published:
>> >>

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

Can you share with us how you resolved the issue, so that other people
who might search the email list for similar issues might benefit?

Thanks,
Thomas

On Mon, May 18, 2015 at 3:39 PM, 陳昱潔  wrote:
> Hi Dr. Yeo:
>
> Thank you very much we already solved the problem!
>
> Very appreciate for your kindness!
>
> Best wishes,
> Annie
>
> 2015-05-18 2:16 GMT-04:00 Thomas Yeo :
>
>> Hi Annie,
>>
>> I am a little unsure why this might happen. Did you inspect if
>> $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot is correct?
>>
>> Cheers,
>> Thomas
>>
>> On Mon, May 18, 2015 at 1:52 PM, 陳昱潔  wrote:
>> > Hi Dr. Yeo :
>> >
>> > Thank you very much for helping us a lot!
>> > I ran the command this below:
>> > mri_surf2surf --srcsubject fsaverage5 --trgsubject 5204 --hemi lh \
>> >--sval-annot
>> > $SUBJECTS_DIR/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot \
>> >--tval
>> > $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot
>> > and after I ran this command:
>> > mris_anatomical_stats -a
>> > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot  -b 5202
>> > rh
>> > All turned out
>> > MRISreadAnnotationIntoArray: vertex index out of range: 892219914
>> > i=352E320A, in_array_size=153173
>> > annot file:
>> > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 892219914
>> > i=352E320A, in_array_size=153173
>> > annot file:
>> > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 892219914
>> > i=352E320A, in_array_size=153173
>> > annot file:
>> > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 892219914
>> > i=352E320A, in_array_size=153173
>> > annot file:
>> > 5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
>> > MRISreadAnnotationIntoArray: vertex index out of range: 892219914
>> > i=352E320A, in_array_size=153173
>> >
>> > Best wishes,
>> > Annie
>> >
>> > 2015-05-15 8:15 GMT-04:00 Thomas Yeo :
>> >
>> >> Hi Annie,
>> >>
>> >> Can you tell us the exact mri_surf2surf command you use?
>> >>
>> >> Cheers,
>> >> Thomas
>> >>
>> >> On Fri, May 15, 2015 at 5:24 PM, 陳昱潔  wrote:
>> >> > Hi Dr. Yeo,
>> >> >
>> >> > Thank you very much for your help! It is the exactly we need!
>> >> > Only a little question that when we ran mris_surf2surf
>> >> > Something seems wrong , but I can't figure out.
>> >> > annot file:
>> >> >
>> >> >
>> >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
>> >> > MRISreadAnnotationIntoArray: vertex index out of range: 152420
>> >> > i=00A4F8DC,
>> >> > in_array_size=10242
>> >> > annot file:
>> >> >
>> >> >
>> >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
>> >> > MRISreadAnnotationIntoArray: vertex index out of range: 152421
>> >> > i=00A4F8DC,
>> >> > in_array_size=10242
>> >> > annot file:
>> >> >
>> >> >
>> >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
>> >> > MRISreadAnnotationIntoArray: vertex index out of range: 152422
>> >> > i=00010101,
>> >> > in_array_size=10242
>> >> > annot file:
>> >> >
>> >> >
>> >> > /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot\
>> >> > reading colortable from annotation file...
>> >> > colortable with 18 entries read (originally MyColorLUT)
>> >> > Reading target surface reg
>> >> > /home/annie/test_run_allindex/5204/surf/lh.sphere.reg
>> >> > Done
>> >> > Mapping Source Volume onto Source Subject Surface
>> >> > surf2surf_nnfr: building source hash (res=16).
>> >> > Surf2Surf: Forward Loop (160564)
>> >> >
>> >> > Surf2Surf: Dividing by number of hits (160564)
>> >> > INFO: nSrcLo

Re: [Freesurfer] Repost: Make liberal ROI masks

[Thomas Yeo]

Hi Martin,

I am a little confused. Can you explain a little more about what you
need? Do you want the freesurfer cortical ROIs dilated into the
surrounding regions like white matter and CSF or something? If so,
then Doug's suggestion sounds reasonable.

In the case of my parcellation, I ran the MNI152 template through
recon-all, which unfortunately resulted in an overly conservative
estimate of gray matter (i.e., the tight mask in
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
Therefore I went through a rather complicated way of generating the
liberal mask by registering the recon-all of 1000 subjects to MNI
space.

Since you appear to be working on an individual subject, the
freesurfer estimate of the cortical ROIs is likely to be quite
accurate. Why might you want to dilate them into CSF or white matter?

Regards,
Thomas

On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve
 wrote:
> There is not an easy way to do that, though Thomas might want to chime
> in. I would probably use the code that generates the wmparc
> (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a
> few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels
>
> On 07/14/2015 08:18 AM, Martin Hebart wrote:
>> Dear Freesurfer users,
>>
>> I would be really happy if someone could help me out on the issue I
>> mentioned below.
>>
>> What I want to do is create non-overlapping anatomical ROI masks that
>> are not restricted to grey matter only.
>>
>> Thanks a lot in advance!
>> Martin
>>
>> -
>>
>> Dear all,
>>
>> I've created non-overlapping ROI masks using
>>
>> mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o
>> rois.nii --temp sub.nii --subject 01
>>
>> Now these ROI masks are actually quite conservative concerning grey
>> matter vs. other structures, i.e. they are only on the grey matter.
>> I've seen more liberal masks e.g. here:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
>>
>> I would like to create similarly liberal non-overlapping ROI masks for
>> all ROIs in the voxel size defined by the image in --temp, but
>> excluding specific tissue types such as white matter, CSF, and other
>> non-grey matter tissue. What would be the best way to do so?
>>
>> Cheers,
>> Martin
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

[Thomas Yeo]

As mentioned by Chris, (2) and (3) are not super clear cut, but you
can perhaps use my resting-state networks (available in FreeSurfer;
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)
as a basic reference. Roughly speaking, for the 7-network
parcellation, the blue cluster corresponds to
somatosensory,motor,auditory, while the purple cluster corresponds to
visual. The remaining networks can be considered
association/heteromodal. The "cream" network can be considered
limbic/paralimbic.

--Thomas


On Fri, Jul 24, 2015 at 12:24 AM, Watson, Christopher
 wrote:
> I have tools in R that can do #1, and network/graph theory analysis on top
> of that. I plan to work on things like #2-3 but haven't yet (e.g. there is
> possibly less consensus if region X is limbic vs. para-limbic, as opposed to
> temporal vs. parietal).
> I can send you something in a few days/a week.
>
> Although, If you read the Destrieux 2010 paper, you will see the regions (in
> the text) separated by lobe, at the least.
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julie Evans
> [julie.evans.st...@gmail.com]
> Sent: Thursday, July 23, 2015 11:39 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] assigning 74 Destrieux parcellations into lobes,
> networks, sensory-motor modalities
>
> Dear FreeSurfer community,
>
> I am a statistician who knows shamefully little about brain anatomy and I am
> writing with a request.
>
>
>
> I don’t have easy access to Freesurfer and the original data but have the
> final text output i.e., the /stats folder, from a large cohort, which
> including *h.aparc.a2009s.stats.
>
>
>
> I have been attempting to assign higher-order labels to the 74 Destrieux
> parcellations.
>
>
>
> 1) Categorizing uniquely into the 4 lobes: frontal, occipital, parietal,
> temporal;
>
>
>
> 2) Categorizing uniquely into “types of networks”: limbic, paralimbic,
> unimodal, heteromodal, subcortical, primary;
>
>
>
> 3) sensory-motor modality: somatosensory, visual, auditory, motor
>
>
>
> As far as I understand these higher-order assignments of the 74
> parcellations are not uncommon although not all cases are clear-cut so some
> knowledge of anatomy is needed (assuming that I am indeed looking at the
> correct level – gyri and sulci in the aparc.a2009s.stats file).
>
>
>
> If so, would anyone mind sharing a text file with the correspondence between
> the 74 parcellations and lobes, network types, and/or modality?
>
>
>
> I’d be very grateful for any guidance and help.
>
>
>
> Thank you kindly,
>
>
> J Evans
>
>
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Re: [Freesurfer] question on Cortical Parcellation Estimated by Intrinsic Functional Connectivity

[Thomas Yeo]

Hi Hong Xin,

Yes. fslview will complain. After you install freesurfer. You can use
freeview to display my parcellation and the fsl template. You should
verify that they align perfectly well. So my parcellation and FSL mni
template are in alignment, but the header information are not the
same.

Since the parcellations are released as part of freesurfer, I am
cc-ing the freesurfer list so other users might benefit from your
question.

Cheers,
Thomas

On Sun, Aug 23, 2015 at 10:30 AM, Hong Xin (SBIC)
 wrote:
> Thanks you very much for the quick response. We use FSL for processing, which 
> displays the parcellations and template/our images in different orientations 
> and we were not able to overlay them due to the different matrix size. I'll 
> install freesurfer and try mri_vol2vol.
> Thanks again.
>
> ____________
> From: Thomas Yeo [thomas@nus.edu.sg]
> Sent: Friday, August 21, 2015 5:36 PM
> To: Hong Xin (SBIC)
> Subject: Re: question on Cortical Parcellation Estimated by Intrinsic 
> Functional Connectivity
>
> Hi Xin,
>
> Actually, the 256x256x256 and 182x218x182 volumes are already in
> alignment. It's just that their header information are different.
> Therefore you do not need to perform an image registration. I suggest
> you use mri_vol2vol, which is a freesurfer function:
>
> mri_vol2vol --mov my256x256x256_parcellation.nii.gz --targ
> 182x182x182_brain.nii.gz --o output.nii.gz --regheader --interp
> nearest
>
> The above command should work. Let me know if you have other issues.
>
> Cheers,
> Thomas
>
> On Fri, Aug 21, 2015 at 5:32 PM, Hong Xin (SBIC)
>  wrote:
>> Hi Prof Yeo,
>>
>>
>>
>> We would like to apply the cortical parcellations to our study. Our images
>> are in the MNI space (matrix size 182x218x182), though the 'parcellations in
>> Nonlinear MNI152 Volume Space' match the MNI template (MNI152_T1_1mm_brain),
>> the labeled image has a different matrix size (256x256x256) and orientation.
>> Since we are not familiar with freesurfer, we wondered if there is a version
>> of the parcellations in the MNI space (with same matrix size and
>> orientation) available? Or we need to make it by ourselves? If so, could you
>> help to check if the following proposed steps are correct: 1. run a rigid
>> body transformation, bring FSL_MNI152_FreeSurferConformed_1mm to
>> MNI152_T1_1mm_brain. 2. apply the transformation to the labeled images (eg,
>> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm).
>>
>>
>>
>> Your input is highly appreciated.
>>
>>
>>
>> Best,
>>
>> Xin
>
> 
>
> Important: This email is confidential and may be privileged. If you are not 
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Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Thomas Yeo]

Hi Ali,

May I confirm that your data is T1 and not functional data? Here's
what you can do to transfer the parcellation to your individual
subject's surface mesh. After that you can use the usual commands to
extract thickness, etc.

In your shell (assuming you are using c shell)

# First set variable s to be subject id
>> set s = 100306_QD95CU_FS

# set freesurfer environmental variable SUBJECTS_DIR to point to where
the data is
>> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/

# use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage

# use "-sval-annot" option to transfer annotation
>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot 
>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot

# use "sval" option to transfer confidence map.
>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>>  --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz

Cheers,
Thomas

On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh  wrote:
> Dear FreeSurfer experts,
>
> I have finished processing a group of brains MR images collected at 7T
> scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
>
> However, we need to get the cortical parcellation based on functional
> network connectivity. So I have downloaded the Atlas data
> (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I have
> few questions which I hope you will be able to help me on.
>
> 1- Do I need to repeat the "recon-all" process?
> 2- If yes, how can I change the default Atlas that freesurfer uses?
> 3- If no, what can I do to get the cortical parcellation based on finctional
> networks from our processed data?
> 4- At the end, shall I use the usual commands to extract the volumes,
> thicknesses ...etc?
>
>
> Many thanks for your help in advance.
>
> Ali
>
>
> --
> Ali M. Al-Radaideh. PhD
> Head of Department of Medical Imaging
> Vice Dean of the Faculty of Allied Health Sciences
> The Hashemite University,
> Zarqa, Jordan
> W.phone +962 5 390 ext.5422, 5355, 5364
> Email: ali.radai...@hu.edu.jo
> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
>
>
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Thomas Yeo]

Hi Ali,

Sorry, I wasn't clear. The 7 and 17 network atlases are released with
FreeSurfer 5.3. In particular, the "annot" files are found in
$FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
already run recon-all using FreeSurfer, then this means that you do
not need to "save" the new atlas anywhere.

The 7 and 17 network atlases are in fsaverage space. You can run the
following commands to transform the atlases to your individual
subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
and the recon-all of this subject is located in
/share/users/imganalysis/yeolab/data/GSP/.

1) The first step is to set the variable SUBJECTS_DIR to point to
where your subject is:

>> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/

2) The second step is to create a symbolic link so that the FreeSurfer
"fsaverage" subject appears to be in your SUBJECTS_DIR

>> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage

3) The final step is to run mri_surf2surf to transform the 7 network
atlas to your subject's native surfaces.

>> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS --hemi lh 
>> --sval-annot 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot 
>> --tval $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot

Note that the above is only for the left hemisphere. You can replace
all the "lh" with "rh" to transform the right hemisphere instead.

Note that the above is for the 7 networks. You can replace all the "7"
with "17" to transform the 17-network atlas instead.

I hope the above is clearer. Let me know if you have other questions.

--Thomas

On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh  wrote:
> Also, could you please direct me in which directory I should save the new
> atlas?
>
> Thanks,
> Ali
>
> On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo  wrote:
>>
>> Hi Ali,
>>
>> May I confirm that your data is T1 and not functional data? Here's
>> what you can do to transfer the parcellation to your individual
>> subject's surface mesh. After that you can use the usual commands to
>> extract thickness, etc.
>>
>> In your shell (assuming you are using c shell)
>>
>> # First set variable s to be subject id
>> >> set s = 100306_QD95CU_FS
>>
>> # set freesurfer environmental variable SUBJECTS_DIR to point to where
>> the data is
>> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>>
>> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>>
>> # use "-sval-annot" option to transfer annotation
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>> >> --sval-annot
>> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
>>
>> # use "sval" option to transfer confidence map.
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
>> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>> >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>>
>> Cheers,
>> Thomas
>>
>> On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh 
>> wrote:
>> > Dear FreeSurfer experts,
>> >
>> > I have finished processing a group of brains MR images collected at 7T
>> > scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
>> >
>> > However, we need to get the cortical parcellation based on functional
>> > network connectivity. So I have downloaded the Atlas data
>> > (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I
>> > have
>> > few questions which I hope you will be able to help me on.
>> >
>> > 1- Do I need to repeat the "recon-all" process?
>> > 2- If yes, how can I change the default Atlas that freesurfer uses?
>> > 3- If no, what can I do to get the cortical parcellation based on
>> > finctional
>> > networks from our processed data?
>> > 4- At the end, shall I use the usual commands to extract the volumes,
>> > thicknesses ...etc?
>> >
>> >
>> > Many thanks for your help in advance.
>> >
>> > Ali
>> >
>> >
>> > --
>> > Ali M. Al-Radaideh. PhD
>> > Head of Department of Medical Imaging
>> > Vice Dean of the Fac

Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Thomas Yeo]

Hi Ali,

It should work with the old processed data.

--Thomas

On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh  wrote:
> Dear Thomas,
>
> Many thanks for your detailed explanation. I will try it and let you know.
>
> One more question please, last year, I processed another set of subjects
> using an older version of FreeSurfer 5.0. Now the old version has been
> replaced with its new one (5.3.0) on the same PC. In other words, my PC has
> the new version of freesurfer 5.3.0 and two sets of processed T1 images. One
> set was processed using the old version of freesurfer which is no longer
> there. The other set was processed using the new version. So, can I
> transform the network atlases to the set of subjects spaces processed last
> year using the old version of freesurfe 5.0.0r? or or I have to re-run the
> recon-all again?
>
> Many thanks in advance and my apology for keeping you busy with my
> questions.
>
> Ali
>
>
> On Sat, Sep 19, 2015 at 3:14 PM, Thomas Yeo  wrote:
>>
>> Hi Ali,
>>
>> Sorry, I wasn't clear. The 7 and 17 network atlases are released with
>> FreeSurfer 5.3. In particular, the "annot" files are found in
>> $FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
>> already run recon-all using FreeSurfer, then this means that you do
>> not need to "save" the new atlas anywhere.
>>
>> The 7 and 17 network atlases are in fsaverage space. You can run the
>> following commands to transform the atlases to your individual
>> subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
>> and the recon-all of this subject is located in
>> /share/users/imganalysis/yeolab/data/GSP/.
>>
>> 1) The first step is to set the variable SUBJECTS_DIR to point to
>> where your subject is:
>>
>> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>>
>> 2) The second step is to create a symbolic link so that the FreeSurfer
>> "fsaverage" subject appears to be in your SUBJECTS_DIR
>>
>> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>>
>> 3) The final step is to run mri_surf2surf to transform the 7 network
>> atlas to your subject's native surfaces.
>>
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS
>> >> --hemi lh --sval-annot
>> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >> --tval 
>> >> $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot
>>
>> Note that the above is only for the left hemisphere. You can replace
>> all the "lh" with "rh" to transform the right hemisphere instead.
>>
>> Note that the above is for the 7 networks. You can replace all the "7"
>> with "17" to transform the 17-network atlas instead.
>>
>> I hope the above is clearer. Let me know if you have other questions.
>>
>> --Thomas
>>
>> On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh 
>> wrote:
>> > Also, could you please direct me in which directory I should save the
>> > new
>> > atlas?
>> >
>> > Thanks,
>> > Ali
>> >
>> > On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo 
>> > wrote:
>> >>
>> >> Hi Ali,
>> >>
>> >> May I confirm that your data is T1 and not functional data? Here's
>> >> what you can do to transfer the parcellation to your individual
>> >> subject's surface mesh. After that you can use the usual commands to
>> >> extract thickness, etc.
>> >>
>> >> In your shell (assuming you are using c shell)
>> >>
>> >> # First set variable s to be subject id
>> >> >> set s = 100306_QD95CU_FS
>> >>
>> >> # set freesurfer environmental variable SUBJECTS_DIR to point to where
>> >> the data is
>> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>> >>
>> >> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>> >>
>> >> # use "-sval-annot" option to transfer annotation
>> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>> >> >> --sval-annot
>> >> >>
>> >> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >> >> --tval $SUBJECTS

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Sabin,

The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
substructures of the cerebellum (e.g., Crus I, etc). Is that what you
want? Or are you looking to use the functional parcels defined in
Buckner 2011?

In addition, I do not know how mri_segstats works, so I cannot verify
how you call the command is correct. Maybe others can provide feedback
here.

However, the Buckner cerebellar parcellations in
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
space. From your command, I assume your data is in MNI305 space. So
you might need to transform the parcellation from MNI152 to MNI305.

Thanks,
Thomas

On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka  wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from Cortical
> ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
> -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
> --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> subCorticalTimeSeries.txt
>
> But I am not sure on how exactly to extract time series from cerebellar
> regions. So if I want to extract time series from regions as described in
> Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in
> FreeSurferCololLUT.txt? If not could you please direct me to processes that
> I can use.
>
> Cheers,
> Sabin Khadka
>
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Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

Hi Bronwyn,

You raise a good point. You can consider creating a cortical mask using
aparc+aseg.mgz and use that to mask the networks.

However, another approach (which might be more accurate) is to take
cortical networks in fsaverage space and transform to your subject's
surface and then transform into your subject's volume:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
$SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*

# Transform from subject's surface into your subject's volume (I am not
super sure about this. You probably want to double check the output is
correct)
>> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
outfile.nii.gz --hemi lh --subject HS_001 **--regheader*

--Thomas

On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs  wrote:

> Hi Mailing List,
>
> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
> steps I plan to take and I am seeking advice as to:
>
> A) Whether this approach is valid.
> B) Steps to take next.
>
>
>
> * Steps 1-3: *
>
> *1. Run MNI152 1mm template through recon-all*
> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
> Yeo2011_MNI152_FS
> recon-all -all -subjid Yeo2011_MNI152_FS
>
> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
> mri_vol2vol --mov
> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>
> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
> --nearest --inv-morph
>
>
> When previously mapping the Choi 2012 straital parcellations, steps 4 and
> 5 were:
>
> 4. *Creating a striatal mask in the native subject's space from
> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
> (26 & 58)*:
> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>
> *5. **Using this mask to mask the choi striatal parcellations*
> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
> Yeo_atlas_subjID_mask.nii.gz
>
>
> Do I need to do a similar thing for the Yeo cortical parcellations and if
> so what regions should I include in the cortical mask?
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
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> to the NeuRA Magazine] 
>
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Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

You should be able to use the 5.3 version.

Regards,
Thomas

On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs  wrote:

> Hi Thomas,
>
> Thanks for your reply.
>
> The fsaverage directory I have for fs v 5.1 does not include the lh and rh
> Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of
> fsaverage. Can I still use the 5.3 version annot files or would I need a
> seperate set processed with version 5.1?
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
> <https://www.facebook.com/NeuroscienceResearchAustralia>[image: Subscribe
> to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe>
> On 23/06/2016 3:17 pm, Thomas Yeo wrote:
>
> Hi Bronwyn,
>
> You raise a good point. You can consider creating a cortical mask using
> aparc+aseg.mgz and use that to mask the networks.
>
> However, another approach (which might be more accurate) is to take
> cortical networks in fsaverage space and transform to your subject's
> surface and then transform into your subject's volume:
>
> # Transform from fsaverage to subject's surface
> >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
> --sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
> $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*
>
> # Transform from subject's surface into your subject's volume (I am not
> super sure about this. You probably want to double check the output is
> correct)
> >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
> outfile.nii.gz --hemi lh --subject HS_001 **--regheader*
>
> --Thomas
>
> On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs 
> wrote:
>
>> Hi Mailing List,
>>
>> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
>> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
>> steps I plan to take and I am seeking advice as to:
>>
>> A) Whether this approach is valid.
>> B) Steps to take next.
>>
>>
>>
>> * Steps 1-3: *
>>
>> *1. Run MNI152 1mm template through recon-all*
>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>> Yeo2011_MNI152_FS
>> recon-all -all -subjid Yeo2011_MNI152_FS
>>
>> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
>> mri_vol2vol --mov
>> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
>> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
>> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>>
>> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
>> --nearest --inv-morph
>>
>>
>> When previously mapping the Choi 2012 straital parcellations, steps 4 and
>> 5 were:
>>
>> 4. *Creating a striatal mask in the native subject's space from
>> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
>> (26 & 58)*:
>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
>> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>>
>> *5. **Using this mask to mask the choi striatal parcellations*
>> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
>> Yeo_atlas_subjID_mask.nii.gz
>>
>>
>> Do I need to do a similar thing for the Yeo cortical parcellations and if
>> so what regions should I include in the cortical mask?
>> --
>>
>> Kind regards,
>>
>> Bronwyn Overs
>> Research Assistant
>> [image: Neuroscience Research Australia]
>>
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> *M* 0411 308 769 *T* +61 2 9399 1883 <%2B61%202%209399%201883>
>> neura.edu.au
>>
>> [image: Follow @neuraustralia on twitter]
>> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
>> <https://www.facebook.com/NeuroscienceResearchAustralia>[image:
>> Subscribe to the NeuRA Magazine]
>> <http://www.neura.edu.au/help-research/subscrib

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Doug,

Would your mri_segstats command work if instead of aseg.mgz, Sabin
passed in the cerbellum parcellation in the same anatomical space as
aseg?

--Thomas

On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
 wrote:
> After you run preproc-sess, there will be a file called register.dof6.dat.
> Map fmri into the anatomical space, something like
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
> fmcpr.anat.nii.gz
>
> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>
> However, I don't think that the aseg has those cerebellum parcellations.
>
> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>
> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I
> process my fmri data with
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
> -per-run -stc odd
> and then to extract ROI time series values I did
>
> mri_segstats --annot fsaverage rh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> subCorticalTimeSeries.txt
>
> Now I am not sure as how to extract cerebellum ROIs (time series as
> described in Buckner et.al 2011)? If there are any other additional steps I
> need to perform ? or if I have to use some other scripts commands (other
> than mri_segstats).
>
>
> Cheers,
> Sabin Khadka
>
> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo  wrote:
>>
>> Hi Sabin,
>>
>> The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
>> substructures of the cerebellum (e.g., Crus I, etc). Is that what you
>> want? Or are you looking to use the functional parcels defined in
>> Buckner 2011?
>>
>> In addition, I do not know how mri_segstats works, so I cannot verify
>> how you call the command is correct. Maybe others can provide feedback
>> here.
>>
>> However, the Buckner cerebellar parcellations in
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
>> space. From your command, I assume your data is in MNI305 space. So
>> you might need to transform the parcellation from MNI152 to MNI305.
>>
>> Thanks,
>> Thomas
>>
>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka 
>> wrote:
>> > Hi all,
>> >
>> > I am trying to extract mean time series BOLD data using FSFAST from
>> > Cortical
>> > ROIs + sub cortical ROIs and cerebellum.
>> >
>> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm
>> > 6
>> > -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
>> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
>> > mri_segstats --annot fsaverage rh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
>> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >
>> > and for cortical time series
>> >
>> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
>> > --id
>> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
>> > 58
>> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> > subCorticalTimeSeries.txt
>> >
>> > But I am not sure on how exactly to extract time series from cerebellar
>> > regions. So if I want to extract time series from regions as described
>> > in
>> > Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628
>> > in
>> > FreeSurferCololLUT.txt? If not could you please direct me to processes
>> > that
>> > I can use.
>> >
>> > Cheers,
>> > Sabin Khadka
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the P

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Doug, thanks.

Hi Sabin, you can use the following steps to transform the Buckner
cerebellum atlas to your subject's native anatomical space and then
follow Doug's instructions (taken and adapted from another user
Bronwyn's email):

1. Run MNI152 1mm template through recon-all
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS

2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
nonlinear volumetric space
mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
BucknerAtlas1mm_FSI.nii.gz --nearest

3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
volumetric space to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph

4. Create a cerebellum gray matter mask in the native subject's space
by applying mri_binarize to aparc+aseg.mgz of the subject
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
cerebellum_mask_subjID.nii.gz

5. Using this mask to mask the Buckner cerebellum parcellations
fslmaths Buckner2011_atlas_subjID.nii.gz -mas
cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz

Regards,
Thomas

On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
 wrote:
> yes
>
>
>
> On 6/24/16 9:19 AM, Thomas Yeo wrote:
>>
>> Hi Doug,
>>
>> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>> passed in the cerbellum parcellation in the same anatomical space as
>> aseg?
>>
>> --Thomas
>>
>> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
>>  wrote:
>>>
>>> After you run preproc-sess, there will be a file called
>>> register.dof6.dat.
>>> Map fmri into the anatomical space, something like
>>>
>>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>>> fmcpr.anat.nii.gz
>>>
>>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>>>
>>> However, I don't think that the aseg has those cerebellum parcellations.
>>>
>>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>>>
>>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
>>> space. I
>>> process my fmri data with
>>>
>>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
>>> -per-run -stc odd
>>> and then to extract ROI time series values I did
>>>
>>> mri_segstats --annot fsaverage rh aparc --i
>>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
>>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>>>
>>> and for cortical time series
>>>
>>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
>>> --id
>>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
>>> 58
>>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>>> subCorticalTimeSeries.txt
>>>
>>> Now I am not sure as how to extract cerebellum ROIs (time series as
>>> described in Buckner et.al 2011)? If there are any other additional steps
>>> I
>>> need to perform ? or if I have to use some other scripts commands (other
>>> than mri_segstats).
>>>
>>>
>>> Cheers,
>>> Sabin Khadka
>>>
>>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo 
>>> wrote:
>>>>
>>>> Hi Sabin,
>>>>
>>>> The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
>>>> substructures of the cerebellum (e.g., Crus I, etc). Is that what you
>>>> want? Or are you looking to use the functional parcels defined in
>>>> Buckner 2011?
>>>>
>>>> In addition, I do not know how mri_segstats works, so I cannot verify
>>>> how you call the command is correct. Maybe others can provide feedback
>>>> here.
>>>>
>>>> However, the Buckner cerebellar parcellations in
>>>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
>>>> space. From your command, I assume your data is in MNI305 space. So
>>>> you might need to transform the parcellation from MNI152 to MNI305.
>>>>
>>>> Thanks,
>>>> Thomas
>>>>
>>>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka 
>>>> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>>

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Sabin,

I think fslmeants should work. But you might need to first run
mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual
ROIs.

Also can you tell us which step generated the error "ERROR: must
specify a segmentation volume"? Is this the final step? Have you tried
overlaying Buckner_atlas_FSSub.nii.gz onto your individual subject in
freeview to check that the previous steps have worked?

Thanks,
Thomas

On Mon, Jun 27, 2016 at 6:53 PM, Sabin Khadka  wrote:
> Hi Thomas- On second thought is it valid to simply do if I want average time
> series of the cerebellum regions?
>
> fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
> avgCerebellum.txt
>
> Is this correct?
>
>
> Cheers,
> Sabin Khadka
>
> On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka 
> wrote:
>>
>> Hi Thomas and Doug-
>>
>> Thanks for you suggestions. Per your suggestions I performed following
>>
>> recon-all -i
>> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>> -subjid Yeo2011_MNI152_FS
>>
>> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS
>>
>> mri_vol2vol --mov
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> \
>> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
>> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest
>>
>> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
>> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
>> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph
>>
>> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
>> cerebellum_mask_FSSub.nii.gz
>>
>> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
>> Buckner_atlas_FSSub
>>
>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>> fmcpr.anat.nii.gz
>>
>> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
>> test.txt
>>
>> However, I got the following error
>> ERROR: must specify a segmentation volume
>>
>> Am I doing anything wrong here. Do you have any suggestions/fixes?
>>
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo  wrote:
>>>
>>> Hi Doug, thanks.
>>>
>>> Hi Sabin, you can use the following steps to transform the Buckner
>>> cerebellum atlas to your subject's native anatomical space and then
>>> follow Doug's instructions (taken and adapted from another user
>>> Bronwyn's email):
>>>
>>> 1. Run MNI152 1mm template through recon-all
>>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>>> Yeo2011_MNI152_FS
>>>
>>> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
>>> nonlinear volumetric space
>>> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
>>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>>> BucknerAtlas1mm_FSI.nii.gz --nearest
>>>
>>> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
>>> volumetric space to each subject:
>>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>>> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
>>> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>>>
>>> 4. Create a cerebellum gray matter mask in the native subject's space
>>> by applying mri_binarize to aparc+aseg.mgz of the subject
>>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
>>> cerebellum_mask_subjID.nii.gz
>>>
>>> 5. Using this mask to mask the Buckner cerebellum parcellations
>>> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
>>> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>>>
>>> Regards,
>>> Thomas
>>>
>>> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>>>  wrote:
>>> > yes
>>> >
>>> >
>>> >
>>> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
>>> >>
>>> >> Hi Doug,
>>> >>
>>> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>>> >> passed in the cerbellum parcellation in the same anatomical space as
>>> >> aseg?
>>> >>
>>> >> --Thomas
>>> >>
>>> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve

Re: [Freesurfer] Failure to use yeo-7/17 networks maps as templates in MRIcron

[Thomas Yeo]

Hi Hsiang-Yuan,

That's because the header information is different. You can do the following:

>> mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ 
>> FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz

The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation
compatible with mricron. Can you let me know if this works.

Thanks,
Thomas

On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin  wrote:
> Hi Prof. Yeo,
>
> I have problems utilizing yeo 7/17 cortical network parcellation maps as
> templates in MRIcron (I aim to use your cortical parcellation maps to
> underlay my findings in order to derive the implications based on iFC
> networks). To be specific, there is an orientation problem in the current
> version of parcellation maps in MNI space.
>
> Thank you for your help in advance.
>
> Best,
> Hsiang-Yuan
>
> --
> Hsiang-Yuan Lin, M.D.
> Attending Psychiatrist & Adjunct Lecturer
> Department of Psychiatry & Child Mental Health Center
> National Taiwan University Hospital and College of Medicine
> email: louisli...@gmail.com
> CV:
> https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
>
>
>
> --
> Hsiang-Yuan Lin, M.D.
> Attending Psychiatrist & Adjunct Lecturer
> Department of Psychiatry & Child Mental Health Center
> National Taiwan University Hospital and College of Medicine
> email: louisli...@gmail.com
> CV:
> https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
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Re: [Freesurfer] Failure to use yeo-7/17 networks maps as templates in MRIcron

[Thomas Yeo]

Hi Hsiang-Yuan,

I do not know how color file works for MRIcron, so I am unable to help.

Regards,
Thomas

On Tue, Jul 5, 2016 at 2:41 AM, Hsiang-Yuan Lin  wrote:
> Hi Thomas,
>
> Thanks for swift instruction. It works well. However, I have further
> question: could I write the color lut into header? Because I used your
> suggested Colorlut information to create a new .lut file and put them into
> MRIcron templates folder with the correctely oriented Yeo2011_7network
> template. But it failed to present the designated color in MRIcron.
>
> Thank you!
>
> Best,
> Hsiang-Yuan
>
> On Mon, Jul 4, 2016 at 4:37 PM, Thomas Yeo  wrote:
>>
>> Hi Hsiang-Yuan,
>>
>> That's because the header information is different. You can do the
>> following:
>>
>> >> mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ
>> >> FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz
>>
>> The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation
>> compatible with mricron. Can you let me know if this works.
>>
>> Thanks,
>> Thomas
>>
>> On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin 
>> wrote:
>> > Hi Prof. Yeo,
>> >
>> > I have problems utilizing yeo 7/17 cortical network parcellation maps as
>> > templates in MRIcron (I aim to use your cortical parcellation maps to
>> > underlay my findings in order to derive the implications based on iFC
>> > networks). To be specific, there is an orientation problem in the
>> > current
>> > version of parcellation maps in MNI space.
>> >
>> > Thank you for your help in advance.
>> >
>> > Best,
>> > Hsiang-Yuan
>> >
>> > --
>> > Hsiang-Yuan Lin, M.D.
>> > Attending Psychiatrist & Adjunct Lecturer
>> > Department of Psychiatry & Child Mental Health Center
>> > National Taiwan University Hospital and College of Medicine
>> > email: louisli...@gmail.com
>> > CV:
>> >
>> > https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
>> > https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
>> >
>> >
>> >
>> > --
>> > Hsiang-Yuan Lin, M.D.
>> > Attending Psychiatrist & Adjunct Lecturer
>> > Department of Psychiatry & Child Mental Health Center
>> > National Taiwan University Hospital and College of Medicine
>> > email: louisli...@gmail.com
>> > CV:
>> >
>> > https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
>> > https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
>
>
>
>
> --
> Hsiang-Yuan Lin, M.D.
> Attending Psychiatrist & Adjunct Lecturer
> Department of Psychiatry & Child Mental Health Center
> National Taiwan University Hospital and College of Medicine
> email: louisli...@gmail.com
> CV:
> https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
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[Freesurfer] fMRI Postdoctoral Fellow

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc with either strong machine learning
background OR system neuroscience background. Prior experience with
fMRI is a plus.

Topics are flexible. Example topics include individual-subject brain
parcellations, relationships between behavior and brain networks,
dynamic functional connectivity, meta-analysis, neural mass modeling,
graph theoretic modeling of brain networks, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in neuroscience, computer science, electrical
engineering, statistics or related fields. The successful applicant
will work with an interdisciplinary team of computer scientists and
neuroscientists.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Labels to MNI152, SPM compatible

[Thomas Yeo]

One possibility is the header information. I looked at the header
information and they are not exactly the same between the template and
atlas. Perhaps you can try the following:

>> mri_convert --targ Template_T1_IXI555_MNI152.nii --mov 
>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz 
>> --regheader --interp nearest --o Yeo2011_headerfixed.nii.gz

Please note that this would involve a nearest interpolation. Hope this
would work.

--Thomas

On Thu, Aug 4, 2016 at 7:06 PM, Matyáš Kuhn  wrote:
> Hi,
>
> I was using Mango and MriCron to view the results. But you are right that in
> freeview it looks just fine :) I saved the yeo atlas image as nifti and it
> is now looking well also on mango and MRIcroN. So I suppose that the problem
> was with analyze format.
>
> Thank you all for the help :)
>
> Matyas
>
>
> Dne 3.8.2016 v 4:43 Thomas Yeo napsal(a):
>
> Hi Matyas,
>
> In freeview, looks fine to me. See attached.
>
> Can you send us your screenshot?
>
> Regards,
> Thomas
>
> On Tue, Aug 2, 2016 at 9:39 PM, Matyáš Kuhn  wrote:
>
> The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
> comes from
> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
> and the description says it is the FSL MNI152 1mm template interpolated
> and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
> (obtained by putting the FSL MNI152 1mm template through recon-all ). So
> I supposed it is in MNI305 after it was processed with freesurfer. When
> I overlap the
> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and
> Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not
> in MNI152.
>
> When I add the --invertmtx then the result is still the same, empty image.
>
> I uploaded those images here:
> https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip ,
> if you want to try yourself.
>
>
> Thank you,
>
> Matyas
>
>
>
> Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):
>
>   From the names, it looks like both the seg vol and the template vol are
> both in mni152. Where did
> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come
> from? One thing you can try is to invert the registration by adding
> --invertmtx to the command line.
>
>
> On 8/2/16 8:18 AM, Matyáš Kuhn wrote:
>
> Hi Freesurfer experts,
>
> I just started to use Freesurfer and I was wondering how can I convert
> images from MNI305 which uses Freesurfer to MNI152 which is used by SPM.
> We would like to get MNI152 template of Yeo parcelation
> ()
> so we can overlay with our results from SPM fMRI analysis.
>
> I tried this:
> mri_label2vol --seg
> /path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
> \
> --temp
> /path_to_analysis/Template_T1_IXI555_MNI152.nii \
> --reg
> $FREESURFER_HOME/average/mni152.register.dat \
> --o /path_to_analysis/output_mni152.nii
>
> which resulted in image full of zeros (so maybe problem with
> registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152
> template which is used by Computational anatomical toolbox 12 for SPM
> from Christian Gaser and his group.
>
> Thanks in advance for any suggestions,
>
> Matyas
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Re: [Freesurfer] questions about split region from the 7 and 17 networks, from huasheng liu

[Thomas Yeo]

Hi Huasheng,

Here you go: 
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip

I am also cc-ing the freesurfer list.

--Thomas

On Tue, Aug 30, 2016 at 11:05 AM, liuhas_20040125
 wrote:
> Dear professor Yeo :
>
>
>
>   My name is Huasheng Liu, I'm from central south university, china.
>
>   I read the emails you wrote to Yu-chieh Chen in freesurfer's mail-archive,
>
> (from:
> https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html)
>
> and you provided a link to files you extracted individual regions from the 7
> and 17 networks:
>
>
>
> " I have previously extracted individual regions from the 7 and 17
> networks. You can download them here
> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0)."
>
>
>
>
>
>   It seems the link has broken, and i can't get zip file, can you kindly
> give me a copy?
>
>
>
>
>
>   Thank you very much for read this email and sorry for occupied your time.
>
>
>
>  Best wishes!
>  Huasheng Liu
>
>
>
> 2016-08-30
> 
> liuhas_20040125
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Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

[Thomas Yeo]

Hi Noam,

This should be a two step procedure, rather than a one-step procedure.
Here's a previous email I sent to the list about warping Choi's
striatum atlas to individual subject's striatum (which I have modified
for the cerebellum for you). Let us know if this works.

1) Assuming you are quite happy with the freesurfer cerebellum
parcellation in your subjects, then I am assuming freesurfer nonlinear
registration (talairach.m3z) is working quite well. Talairach.m3z
warps your subject to an internal freesurfer space (kinda like MNI305,
but not quite). Let's say the freesurfer recon-all output is at
/SUBJECT_FS/

2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the
MNI152 1mm template to the internal freesurfer space. Let's say the
freesurfer recon-all output is at /MNI152_FS/

3) Then do the following:

a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
2mm resolution to the 1mm MNI152 template:

>> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz 
>> --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest

Notice that I use norm.mgz of the MNI template rather than the
original MNI template. norm.mgz is the 256 x 256 x 256 conformed
version of the MNI template that recon-all puts through.

b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ 
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
>> Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest

c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS 
>> --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z --o 
>> Buckner_atlas_subject.nii.gz --interp nearest --inv-morph

This is not optimal because of the double interpolation. You might
want to use the MNI template instead of the Buckner_atlas to test the
above, so you can check the goodness of the warp. The final warped MNI
template should hopefully look identical to your subject. If that
works, then use the Buckner_atlas. Note that mri_vol2vol does not work
properly for talairach.m3z below version 5, so you should use version
5x mri_vol2vol.

Regards,
Thomas

On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam  wrote:
> Dear group,
> I'm trying to morph the Buckner2011 cerebellum segmentation map from MNI152
> to subject's space:
> mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ
> Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z
> talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest
> --inv-morph
> It worked with the 17 networks, but didn't work with the 7 networks version.
> Any ideas? This is really strange.
>
> Thanks,
> Noam
> (function(){(function n(e) { "use strict"; function t(e) { if (e.parentNode)
> if (e.childNodes.length > 1) { for (var t =
> document.createDocumentFragment(); e.childNodes.length > 0; ) { var n =
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> { var i = o.call(e, t); if (e.classList.contains("mceContentBody"))
> i.innerHTML = e.innerHTML, n(i); else try { r(i); } catch (a) {} return i;
> }, r(e); }
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> })()
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[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms
for large-scale publicly available MRI and behavioral data. Experience
with probabilistic machine learning (aka graphical models) or deep
learning is a plus.

The ultimate goal is automatic scientific discovery (see recent paper
from our lab: http://www.pnas.org/content/113/42/E6535). Topics are
flexible, e.g., multi-modal fusion, individual-subject brain
parcellation, individual subject behavior prediction, dynamic
functional connectivity, meta-analysis, neural mass modeling,
multi-scale neuroscience, graph theory, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Postdoctoral fellow in mental disorder subtypes

[Thomas Yeo]

Dear All,

I am looking for a neuroscience/psychology postdoc to apply machine
learning algorithms (possibly developed in our lab) to discover and
understand mental disorder subtypes from existing large-scale public
databases.

See recent example from our lab
(http://www.pnas.org/content/113/42/E6535). Experience with
psychiatric disorders (especially ASD and ADHD) is a plus, but not
required.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in neuroscience, psychology or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists. Programming experience is
required. He or she does NOT need to code a new algorithm, but must be
able to apply existing code (or modify existing code) for his or her
project.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Ph.D. student openings

[Thomas Yeo]

Hi,

I am looking to recruit talented students to develop novel image
analysis and machine learning algorithms for the Human Connectome
Project data.

This is my research webpage: https://sites.google.com/site/yeoyeo02/.
See more information below.

Regards,
Thomas

Application Deadline: Nov 1st, 2013 in order to start in Fall 2014

Requirements: Bachelor's or Master's degree in computer science,
electrical engineering, statistics or related fields. Ideal candidates
should be highly motivated, and have research experience and/or
excellent grades.

Compensation: Graduate Student Fellowship

Institutes: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).
Successful candidates may be required to travel between Singapore and
the U.S. for certain projects.

Contact: Interested candidates should email Thomas
(ytho...@csail.mit.edu) with CV and/or questions.
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[Freesurfer] postdoc opening

[Thomas Yeo]

Hi,

I am looking to hire talented postdocs to develop novel image analysis
and machine learning algorithms for the Human Connectome Project data.

This is my research webpage: https://sites.google.com/site/yeoyeo02/.
See more information below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics or related fields. Candidates should have previously
published research in image processing or statistical analysis,
preferably in biomedical applications.

Compensation: Competitive and commensurate with experience

Institutes: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).
Successful candidates may be required to travel between Singapore and
the U.S. for certain projects.

Contact: Interested candidates should email Thomas
(ytho...@csail.mit.edu) with CV and/or questions. To apply, please
send cover letter, CV and names/contact information of 3 people who
can provide letters of reference.
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Re: [Freesurfer] MNI152 to 305 conversion

[Thomas Yeo]

Hi Doug,

except Paul was saying the mni305.cor.mgz does not show up correctly
in freeview as well. Doesn't freeview handle header orientation
information properly?

--Thomas

On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve
 wrote:
> Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a
> problem with the visualization tools you are using. Have you contacted the
> developers? I think the data are fine and the information in the header is
> sufficient for a visualization tool to orient it properly (as freeview and
> tkmedit do). I know that fslview will not reorient but puts little letters
> on the side of the image to tell you what the orientation is. I think they
> also have tools to reorient so that it is displayed more reasonably. Have
> you looked into that?
> doug
>
> ps. You can try using the reorder feature in mri_convert, but it will be
> trial and error.
>
>
>
>
>
> On 10/01/2013 11:55 AM, Paul Beach wrote:
>>
>> Ah! Yes. I changed directories to my subjects_dir and the command worked.
>>
>> I then re-tried my original mri_vol2vol script.
>> /
>> /
>> /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz \/
>> /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/
>> /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/
>> /--inv --o FSL_MNI305_2mm.nii.gz/
>> /
>> /
>> Unfortunately I'm getting the same mis-orientation result in AFNI,
>> freeview, and fslview.
>>
>>
>> On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo > <mailto:ytho...@csail.mit.edu>> wrote:
>>
>> Oh I see. You probably don't have write access to the current
>> directory (which I assume to be
>>
>> //extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/,
>> so it can't write out mni305.nii.gz. Write out mni305.nii.gz to
>> another directory.
>>
>> --Thomas
>>
>>
>> On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach > <mailto:pabea...@gmail.com>> wrote:
>>
>> I'm getting the same error, despite doing just that.  :-/
>>
>> /[beachpau@gauss mri.2mm]$ mri_convert
>>
>> /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz
>> mni305.nii.gz/
>> /mri_convert
>>
>> /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz
>> mni305.nii.gz /
>> /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/
>> /reading from
>>
>> /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../
>> /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/
>> /i_ras = (-1, 0, 0)/
>> /j_ras = (0, 0, -1)/
>> /k_ras = (0, 1, 0)/
>> /writing to mni305.nii.gz.../
>> /niiWrite(): error opening file mni305.nii.gz/
>> /ERROR: failure writing mni305.nii.gz/
>>
>>
>>
>> On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo
>> mailto:ytho...@csail.mit.edu>> wrote:
>>
>> Hi Paul,
>>
>> You have to give it the full path:
>>
>> /mri_convert
>>
>> ///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz
>> mni305.nii.gz/
>> /
>> /
>> /--Thomas/
>>
>>
>> On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach
>> mailto:pabea...@gmail.com>> wrote:
>>
>> The mri_convert command did not work...
>> /
>> /
>> /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz
>> mni305.nii.gz/
>> /mri_convert mni305.cor.mgz mni305.nii.gz /
>> /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
>> mreuter Exp $/
>> /reading from mni305.cor.mgz.../
>> /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/
>> /i_ras = (-1, 0, 0)/
>> /j_ras = (0, 0, -1)/
>> /k_ras = (0, 1, 0)/
>> /writing to mni305.nii.gz.../
>> /niiWrite(): error opening file mni305.nii.gz/
>> /ERROR: failure writing mni305.nii.gz/
>>
>>
>>
>> On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo
>> mailto:ytho...@csail.mit.edu>>
>> wrote:
>>
>> Hi Paul,
>>
>&g

Re: [Freesurfer] Cerebellar subdivisions

[Thomas Yeo]

I am not sure about the lobule subdivisions, but there is a cerebellar
subdivisions based on functional connectivity since 5.2. See 5.2
release notes (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes).

--Thomas

On Mon, Oct 7, 2013 at 11:23 PM, Alan Francis  wrote:
> Hi Bruce et al,
>
> Is the parcellation of the cerebellar subdivisions in the works for the next
> version of FS? Is there an ETA for this?
>
> thanks so much,
>
> Alan
>
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[Freesurfer] Fwd: 2nd Whistler Scientific Workshop on Brain Function, March 9-12, 2014

[Thomas Yeo]

-- Forwarded message --
From: Todd Constable 
Date: Thu, Oct 17, 2013 at 9:25 AM
Subject: 2nd Whistler Scientific Workshop on Brain Function, March 9-12, 2014
To: Todd Constable 
Cc: Todd Constable 



The 2nd Whistler Scientific Workshop on Brain Functional Organization,
Connectivity and Behavior
Whistler, BC, Canada  March 9-12, 2014

There has been an explosion of activity recently in the area of
functional MRI and connectivity mapping and this small workshop in the
beautiful town of Whistler BC is aimed at exploring the latest
breakthroughs in analysis approaches, models, and applications.
Emphasis will be on methods, the relationship of network measures to
behavior, and the implications of network mapping in terms of
broadening our understanding of functional neuroanatomy and basic
neuroscience.

The workshop will be kept small (less than 100 attendees) in order to
facilitate discussion amongst all participants so please register
early to ensure a spot.

Abstracts: One page Abstracts for proffered talks or posters can be
submitted to:lesley.nad...@yale.edu.

Topics:

1. Functional connectivity methods - network measures
2. Connectivity and Behavior
3. Integrated structural and functional connectivity – methods &
stationarity and spectral components
4. Clinical applications of functional connectivity or multimodal
measures of connectivity
5. Neuroanatomy and brain mapping

For more information and to register please visit: fmriworkshop.yale.edu

Target Audience:
Experts in functional brain imaging and connectivity mapping,
neuroscientists, psychologists, clinicians, and trainees (pre- and
postdoctoral fellows, residents and clinical fellows), with an
interest in brain function, functional organization, and neuroimaging.

Organizing Committee:

R. Todd Constable, Committee Chair, Yale University, New Haven, CT, USA
Karla Miller, Oxford Centre for Functional MRI of the Brain, Oxford
University, UK
Marvin Chun, Yale University, Department of Psychology, New Haven, CT USA
Bruce Pike, Division of Image Science, University of Calgary, Alberta, Canada
Xiaoping Hu, Coulter Dept. of BME at Georgia Tech and Emory, Atlanta, GA USA

Invited Speakers:

Michael Breakspear, Systems Neuroscience, Queensland Inst. of Med. Research, AU
Mark Chiew, Oxford University Centre for Functional MRI of the Brain, Oxford, UK
Jessica Damoiseaux, Institute of Gerontology, Wayne State University,
Detroit, MI
Manus Donahue, Vanderbilt University Institute of Imaging Science, Nashville, TN
Lila Davachi, Center for Neural Science & Center for Brain Imaging, NYU, NY, NY
Maxime Guye, Centre de Resonance Magnetique Biologique et Medicale, France
Xiaoping Hu, Coulter Dept. of BME at Georgia Tech and Emory, Atlanta, GA
Angela Laird, Department of Physics, Florida International University, Miami, Fl
Tom Liu, USD Center for Functional MRI, La Jolla, CA
Zhongming Liu, Biomedical Engineering, Purdue University, West
Lafayette, Indiana
Joseph Mandeville, Martinos Center for Biomedical Imaging, Harvard, Boston, MA
Galit Pelled, Kennedy Krieger Institute, Baltimore, MD
Amir Shmuel, Montreal Neurological Institute, McGill University,
Montreal, Canada
Nick Turk-Browne, Department of Psychology, Princeton University, Princeton, NJ
Martijn van den Heuvel, Dept. of Psychiatry, Rudolf Magnus Inst,
Utrecht, Netherlands
Gael Varoquaux, NeuroSpin, CEA Saclay, Gif-sur-Yvette, France
Thomas Yeo, Dept. of Electrical and Computer Engineering, Natl. Univ.
of Singapore


Program:

Sunday, March 9  Check-in: noon – 6pm
6:00 – 8:00pm Opening cocktail party

Monday, March 10
7:30-8:30amBreakfast

Session 1Session Chair:

8:30 – 9:00am Gael Varoquaux: “What can we learn of brain
connectivity by
mining resting-state?”

9:00 – 9:30am     Thomas Yeo: “Organization of the Human Brain
Estimated by
Intrinsic Functional Connectivity”

9:30 – 10:00am   Tom Liu: “What can we learn from multimodal
Imaging (fMRI,
EEG, MEG) of resting state brain activity?”

10:00 – 10:30am Coffee

10:30-12 noon Proffered talks 10 – 15min each depending
upon how many

12 noon   Box Lunch

12:00 – 4:30pm   Break

4:30 – 5:00pm Coffee

Session 2Session Chair:

5:00 – 5:30pm Galit Pelled: “Mapping and manipulating
neuroplasticity”

5:30 – 6:00pm Lila Davachi: “Dynamic alterations in
low-frequency BOLD
connectivity related to memory
encoding, retrieval and
consolidation”

6:00 – 6:30pm Nick Turk-Browne: “Attention and modulation
of connectivity
between high and low level visual
areas (or) category-specific
connectivity in the visual cortex”

6:30 – 7:15pm Proffer

Re: [Freesurfer] Choi2012 convert to FSL MNI152 2mm

[Thomas Yeo]

Hi Doug, the Choi volume is in MNI152 space, not MNI305 space.

Hi Kathy, the correct command is "mri_vol2vol --mov $input --targ
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o
output1.nii.gz --no-save-reg --interp nearest"

Please note the use of the "--regheader" flag. The Choi volume is in
exactly the SAME space as the
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the
header information is different. Therefore the "regheader" flag takes
care of that.

--Thomas

On Mon, Nov 11, 2013 at 7:40 PM, Douglas Greve
 wrote:
>
> Is the Choi2012 volume in fsaverage/mni305 space? If so, then the 2nd
> command is the right one. Use mri_binarize with the --match option to
> create separate masks.
> doug
>
>
> On 11/11/13 2:24 PM, Kathy L. Pearson wrote:
>> To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I 
>> have tried both of the mri_vol2vol commands below.  The results as shown in 
>> freeview are offset by several voxels from the original.  Is there a 
>> transform or an intermediate step that can make this work -- or a different 
>> command?  Also, is there a recommended way to extract each individual value 
>> (here 1 ... 7) to create separate masks in FSL 2mm space?
>>
>> Thanks for any advice,
>>
>> Kathy Pearson
>>
>> #!/bin/bash
>> input=$FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152/Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>> mri_vol2vol --mov $input --targ 
>> $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg 
>> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o 
>> output1.nii.gz --no-save-reg --interp nearest --precision uchar
>> mri_vol2vol --targ $input --mov 
>> $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --inv --reg 
>> $FREESURFER_HOME/average/mni152.register.dat --o output2.nii.gz 
>> --no-save-reg --interp nearest --precision uchar
>>
>> # Compare results
>> freeview $input output1.nii.gz output2.nii.gz&
>>
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>>
>>
>
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Re: [Freesurfer] Inquiry about Choi's striatum parcellations.

[Thomas Yeo]

Hi Sooyun,

To convert the Choi's parcellation to the MNI152 template from FSL, you
should just use mri_vol2vol, rather than FIRST. The command is as follows: "
mri_vol2vol --mov original_choi_MNI152_parcellation.nii.gz --targ
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o
FSL_choi_MNI152_parcellation.nii.gz --no-save-reg --interp nearest"

Please note the use of the "--regheader" flag. The Choi volume is in exactly
the SAME space as the $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz,
it's just that the header information is different. Therefore the
"regheader" flag takes care of that.

Cheers,
Thomas


On Mon, Jan 27, 2014 at 4:31 PM, 조수연  wrote:

>  Hello,
>
> I'm a FreeSurfer beginner and would like to ask a question about Choi's
> stratium parcellations. I was doing a research to incoorporate the
> parcellations by Choi on my subjects' images to delve further to understand
> the distincitve characteristics of each parcels. I decided to use the
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz. Since my
> images were on the standardized model from FSL, I transformed Choi's image
> to the MNI standard using FIRST of FSL. Since both images were now on the
> same MNI space, I viewed both of them on FSL to make sure that the Loose
> mask covered my image completely, but found that the tail bit of my image
> was a couple of pixels too longer than Choi's Loosened mask. Do you think
> there is a way that I can further "loosen" up Choi's image to fit my image?
> Or can you recommend me a different solution to this problem?
>
> I'll wait for your reply. Thanks!
>
>
>
> Sincerely, Sooyun Cho.
>
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Re: [Freesurfer] Yeo parcellation

[Thomas Yeo]

Hi Stefano,

A) From FreeSurfer 5.2 onwards, the Yeo parcellation files can be
found inside $FREESURFER_HOME/subjects/fsaverage/label/, so you can
simply use those files there instead of downloading from the wiki.

B) You can use mri_surf2surf to transform the annot files from the
fsaverage "subject" to the individual subjects' surface. There is an
example of how to do it if you run "mri_surf2surf --help"

C) Once you have created the subject's specific annot file from part
B, I believe you must first run mris_anatomical_stats, and then run
aparcstats2table. However, I am not sure about this, so someone on the
list should correct me if I am wrong!

Regards,
Thomas

On Fri, Feb 7, 2014 at 3:58 PM,   wrote:
> Hi list,
>
> I have download the files of Yeo parcellation from
> ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip.
>
> I have two questions, please.
>
> A- Which is the directory where I should put these files?
> B-I have already run by recon-all -all all my subjects. How can I added to
> them Yeo parcellation?
> C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is
> possible with aparcstats2table?
>
> Thanks.
>
> Regards,
>
>
> Stefano
>
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Re: [Freesurfer] Choi's parcellation expansion inquiry

[Thomas Yeo]

Hi Sooyun,

It is possible that tri-linear might work better, but I have to caution
that you will get non-integer values. Have you tried mri_label2vol?
According to Doug in the last email, mri_label2vol might work better than
mri_vol2vol.

My suggestion is to first verify whether the transformation from Choi
parcellation to the subject's native space is good enough. To do that,
instead of transforming the Choi parcellation, try transforming the MNI152
template accompanying the Choi's parcellation (NOT the FSL MNI152
template). If the transformed MNI152 template does not match your subject's
native anatomy to your liking, then you need to improve the transformations.

Again, can you clarify where you are obtaining the transformation matrices?
Recall that I previously told you that to convert the Choi's parcellation
to the MNI152 template from FSL, you should just use mri_vol2vol, rather
than FIRST. The command is as follows: "mri_vol2vol --mov
original_choi_MNI152_parcellation.nii.gz --targ
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o
FSL_choi_MNI152_parcellation.nii.gz --no-save-reg --interp nearest". And
the reason is that the Choi volume is in exactly the SAME space as the
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header
information is different. Therefore the "regheader" flag takes care of that.

Cheers,
Thomas


On Tue, Feb 11, 2014 at 2:03 PM, 조수연  wrote:

>  Hi, Thomas.
>
>
>
>
>
> I have circled the unmasked regions in the image with a red brush tool.
> The yellow-red regions are the FreeSurfer space->MNI152 space->Subject
> space transformed Choi's loose mask files, and the blue regions are the
> subject's subcortical areas. My current ROI is the caudate and the putamen.
> As you can see, there are multiple regions where the labels aren't big
> enough to cover my subject data. I checked the original Choi's
> parcellations in the original space and the MNI152 space but it's hard to
> check whether the label in the specific location of my interest is missing
> or not because the voxel numbers and dementions are different per space,
> thus is hard to get the specific coordinates that lacks mask.
>
> I discussed with my lab members and concluded maybe the problem lies when
> we are transferring the image from one space to another in that we used the
> nearest neighbour when applying the transformation matrix. We are planning
> to use tri-lear for interpolation instead so that the achieved image has a
> looser intensity specificaton, so that it helps us to specify the lables of
> the subject's regions which are not covered by Choi's masks. Hope this
> helps.
>
> If you have any suggestions as of how to morph Choi's images best to our
> subject's fit, please do inform me. Thanks!
>
>
>
> Best regards, Sooyun.
>
>
>
>
>
> ---원본메일---
> 보낸사람 : Thomas Yeo 
> 받는사람: 조수연
> 참 조: freesurfer 
> 보낸날짜: 2014-02-11 00:11:48 GMT +0900 (ROK)
> 제목: Re: [Freesurfer] Choi's parcellation expansion inquiry
>
>
> Hi Sooyun,
>
> Which is the sky blue region you are referring to? Can you place your
> fslview cursor in the location where you think is missing the label?
>
> Can you visually inspect the original Choi's parcellation to see if the
> label is also missing at the corresponding MNI152 location? If the label is
> not missing, then perhaps your transformation is not doing its job, which I
> suspect might be the problem since the loose mask in Choi's parcellation is
> already pretty loose.
>
> Regards,
> Thomas
>
>
> On Mon, Feb 10, 2014 at 12:20 PM, 조수연  wrote:
>
>>  Hi, all.
>>
>> I'm trying to apply Choi's parcellations onto my subjects' data. I used
>> the 7-Network loose mask but it turns out that even the loose mask isn't
>> capable of covering up the ROI.
>>
>> Is there a way I can further "expand" the loose mask and make it "looser"?
>>
>> The uncovered areas of my subject's image are colored skyblue. The rest
>> are parcellated segments of Choi's image.
>>
>> FYI Choi's FreeSurfer grid images were linearly transformed by concat
>> matrix which shifts FreeSurfer grid to Standard MNI152 grid to our
>> subject's grid.
>>
>>
>>
>> Thanks.
>>
>>
>>
>> Best regards, Sooyun.
>>
>> ___
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>>
>>
>> The information in this e-mail i

[Freesurfer] postdoc in brain image analysis

[Thomas Yeo]

Dear All,

I am looking for a postdoc to work on brain image analysis, e.g.,
dynamic functional connectivity. See more information below.

Regards,
Thomas


Job Title: Postdoctoral Fellow in Brain Image Analysis

Project: Develop novel image analysis and machine learning tools for
brain image analysis, (e.g. Dynamic Functional Connectivity).

Research Webpage: http://yeolab.weebly.com/research.html

Requirements: Ph.D. in computer science, electrical engineering,
statistics or related fields. Candidates should have previously
published research in image processing, computer vision, statistical
or machine learning. Experience with functional MRI is preferred (but
not required).

Compensation: Competitive and commensurate with experience

Institutes: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).
Successful candidates may be required to travel between Singapore and
Harvard Medical School for certain projects.

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: 1st May, 2014
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Re: [Freesurfer] applying Yeo atlas to individual brains

[Thomas Yeo]

Hi Jeff,

I am a little unsure myself since I usually work with data mapped to
fsaverage space. I think you might want to use mri_surf2surf, since
there's a "--sval-annot" option. It's hard for me to check now because
I am away at a conference.

Can someone chime in if mri_surf2surf is wrong?

Thanks,
Thomas





On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen  wrote:
> What I need are the ?h.Yeo.annot files for the individual subjects, similar 
> to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will 
> mri_label2labe give me that directly?
>
> Thanks,
> -Jeff
>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Monday, March 10, 2014 9:50 AM
> To: Jeff Eriksen
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] applying Yeo atlas to individual brains
>
> Hi Jeff
>
> you should be able to use mri_label2label to map the Yeo atlas from fsaverage 
> to any subject.
>
> cheers
> Bruce
> On Mon, 10 Mar 2014, Jeff Eriksen wrote:
>
>>
>> Our lab has a need to apply the Yeo atlas to individual brains. As I
>> understand it, Yeo atlas is only currently available for the FSAverage
>> brain. Any plans to incorporate Yeo on to the default FS segmentation,
>> or have it available as an option?
>>
>>
>>
>> -Jeff Eriksen
>>
>>
>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom it is 
> addressed. If you believe this e-mail was sent to you in error and the e-mail 
> contains patient information, please contact the Partners Compliance HelpLine 
> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
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Re: [Freesurfer] fsaverage mesh has duplicate pt

[Thomas Yeo]

Can confirm also true for lh.white, but not lh.sphere and lh.inflated.

--Thomas

On Thu, Apr 10, 2014 at 1:11 PM, Xuelong Zhao  wrote:
>
> Hi,
>
> I loaded the lh.orig cortex for fsaverage into Matlab. My colleague and I
> found that it actually has a duplicate point.
>
> The index of the duplicate points are:
>
> 1
> 40970
>
> I checked that both have the same vertices coordinates:
>
>   -36.7233  -18.4039   64.3611
>
>
> I'm not sure if this is intentional or not but wanted to draw the freesurfer
> community's attention to this in case it is a bug. Also, I believe a similar
> issue is present for fsaverage's lh.pial and rh.orig (I haven't checked
> other cortices).
>
> Regards,
>
> AZ
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
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[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms for fMRI.

Topics are flexible. Example topics include dynamic functional
connectivity, meta-analysis, neural mass modeling, monkey-human
homologies, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Erica,

You can try this link:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip

Regards,
Thomas

On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung  wrote:
> Dear Prof. Yeo,
>
> I would like to extract the brain regions of the functional canonical
> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have
> provided the split regions of 7&17 Network in previous discussion string.
> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
>  )
>
> However, the dropbox download link you offered has expired.
> Would you mind uploading it again?
>
> Thank you very much.
>
> Erica
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[Freesurfer] OHBM white paper on best practices in Data Analytics and Sharing

[Thomas Yeo]

Dear FreeSurfer List,

In 2014 OHBM Council created the Committee on Best Practices in Data
Analysis and Sharing (COBIDAS) to identify best practices of data
analysis and data sharing in the brain mapping community.

The COBIDAS committee has prepared a white paper organizing these
practices and seek input from the OHBM community before ultimately
publishing these recommendations.

You can find the whitepaper here:
http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3668.
Feedback can be provided here: http://cobidas.wordpress.com/

Regards,
Thomas
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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Richard,

Sorry. My original reply was rejected by the list. Resending.

In the mri_surf2surf command, Instead of the srcsubject being
fsaverage, can you try using the srcsubject as fsaverage5 instead?

Alternatively, you can try running mri_surf2surf twice. Once to
upsample the fsaverage5 annot to fsaverage and then run the
mri_surf2surf command from your email. (This might actually work
better).

Thanks,
Thomas

On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard
 wrote:
> Hi Professor Yeo,
>
>
>
> Thanks for providing a link to your split region MNI space files.
>
>
>
> Could you please advise on how to get these labels into subject native
> space?
>
>
>
> If using the standard version of the network labels that comes packaged with
> Freesurfer 5.3.0, I can get the annotation file into native space quite
> easily with the following command:
>
>
>
>
>
> mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh
> --sval-annot
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot
>
>
>
> However, in the dropbox link you posted, it doesn’t seem that there is a
> .annot file compatible with fsaverage. The fsaverage5 version is present,
> but if I try slotting the fsaverage5 .annot file into the above call to
> mri_surf2surf, I get disastrous results.
>
>
>
> Do you perhaps have a .annot file for the upsampled (and split) network
> labels? Or perhaps there’s an easier way to achieve what I’m after. I notice
> that you have provided a .nii file for the network ROIs that is in the same
> space as fsaverage, perhaps this file can be warped to native space somehow?
>
>
>
> Best wishes,
>
>
>
> Richard Parker
>
> King’s College London
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi Erica,
>
>
>
> You can try this link:
>
> https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip
>
>
>
> Regards,
>
> Thomas
>
>
>
> On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung 
> wrote:
>
>> Dear Prof. Yeo,
>
>>
>
>> I would like to extract the brain regions of the functional canonical
>
>> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you
>> have
>
>> provided the split regions of 7&17 Network in previous discussion string.
>
>>
>> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
>
>>  )
>
>>
>
>> However, the dropbox download link you offered has expired.
>
>> Would you mind uploading it again?
>
>>
>
>> Thank you very much.
>
>>
>
>> Erica
>
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Richard,

This occurs because the gaps exist in the original fsaverage5
split_component parcellation. As explained in the documentation text
file (Yeo_JNeurophysiol11_SplitLabels_README which should also be
included in the zip file), one of the steps taken to generate
*.split_components.annot involved removing vertices at the boundaries
between parcels. This is to reduce the mixing of signals across
parcels, e.g., due to spatial smoothing.

You can see these gaps if you plot the fsaverage5 annot on the
fsaverage5 subject. Therefore when the parcellation is upsampled from
fsaverage5 to fsaverage, the gaps are propagated. I admit the gaps do
not look very visually pleasing because going from fsaverage5 to
fsaverage involved an upsampling factor of 4. However, I think the
gaps should not be detrimental to your analysis.

How does the parcellation look when you transfer the (upsampled)
fsaverage parcellation to the individual subject's surface?

Regards,
Thomas

On Mon, Dec 14, 2015 at 6:43 PM, Parker, Richard
 wrote:
> Hi Prof,
>
>
> Thanks for the speedy reply,
>
>
> When you specify fsaverage5 as -srcsubject and your own subject as
> -trgsubject, the code executes but the resulting .annot file looks like a
> mess.
>
>
> Your proposed two-step call to mri_surf2surf seems more promising. If I run
> the following:
>
>
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject fsaverage --hemi lh
> --sval-annot
> fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval
> ./lh.YeoUpsample.annot
>
> I end up with a .annot file in the same space as fsaverage, but there seem
> to be large gaps between the labels. Here's a screenshot of what I mean:
>
>
> http://imgur.com/VvqYEWx
>
>
> Do you have any suggestions on how to account for this? Is there some
> unresolved mismatch between the number of vertices following upsampling,
> perhaps?
>
>
> Best wishes,
>
>
> Richard
>
>
>
>
>
>
>
>
>
>
> Hi Richard,
>
> Sorry. My original reply was rejected by the list. Resending.
>
> In the mri_surf2surf command, Instead of the srcsubject being
> fsaverage, can you try using the srcsubject as fsaverage5 instead?
>
> Alternatively, you can try running mri_surf2surf twice. Once to
> upsample the fsaverage5 annot to fsaverage and then run the
> mri_surf2surf command from your email. (This might actually work
> better).
>
> Thanks,
> Thomas
>
> On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard
>  wrote:
>> Hi Professor Yeo,
>>
>>
>>
>> Thanks for providing a link to your split region MNI space files.
>>
>>
>>
>> Could you please advise on how to get these labels into subject native
>> space?
>>
>>
>>
>> If using the standard version of the network labels that comes packaged
>> with
>> Freesurfer 5.3.0, I can get the annotation file into native space quite
>> easily with the following command:
>>
>>
>>
>>
>>
>> mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh
>> --sval-annot
>>
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot
>> --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot
>>
>>
>>
>> However, in the dropbox link you posted, it doesn’t seem that there is a
>> .annot file compatible with fsaverage. The fsaverage5 version is present,
>> but if I try slotting the fsaverage5 .annot file into the above call to
>> mri_surf2surf, I get disastrous results.
>>
>>
>>
>> Do you perhaps have a .annot file for the upsampled (and split) network
>> labels? Or perhaps there’s an easier way to achieve what I’m after. I
>> notice
>> that you have provided a .nii file for the network ROIs that is in the
>> same
>> space as fsaverage, perhaps this file can be warped to native space
>> somehow?
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Richard Parker
>>
>> King’s College London
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi Erica,
>>
>>
>>
>> You can try this link:
>>
>>
>> https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip
>>
>>
>>
>> Regards,
>>
>> Thomas
>>
>>
>>
>> On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung 
>> wrote:
>>
>>> Dear Prof. Yeo,
>>
>>>
>>
>>> I would like to extract the brain regions of the functional canonical
>>
>>> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you
>>> have
>>
>>> provided the split regions of 7&17 Network in previous discussion string.
>>
>>>
>>>
>>> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
>>
>>>  )
>>
>>>
>>
>>> However, the dropbox download link you offered has expired.
>>
>>> Would you mind uploading it again?
>>
>>>
>>
>>> Thank you very much.
>>
>>>
>>
>>> Erica
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient informat

Re: [Freesurfer] about functional ROIs

[Thomas Yeo]

Hi Jintao,

This might be a header error in the original files. The error is not
apparent in the FreeSurfer or FSL environment, but might be problematic
with mricron (completely my fault).

Can you try the files from this zip file instead:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation_MICRON.zip
(courtesy of Chris Rorden).

Please let me know if this resolves your issues.

Regards,
Thomas

On Thu, Dec 31, 2015 at 10:23 AM,  wrote:

>
>
> Dear Professor Yeo,
>
>
>
> My name is Sheng Jintao, and I am a master in China.
>
> Recently, I download the ‘Resting State Cortical Parcellation in nonlinear
> MNI152 space’ in
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
> But when I opened images and found they are very stange. Just like this
> sectional drawing. And I don’t know why, therefore, I would love to consult
> you.
>
> Thank you, and I look forward to hearing from you.
>
>
>
> Best wishes,
>
> Jintao
>
>
>
>
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Re: [Freesurfer] 答复: about functional ROIs

[Thomas Yeo]

Hi Jintao,

The difference comes from the fact that the MNI template I used is 256 x
256 x 256, which was obtained by passing the FSL MNI152 template through
the FreeSurfer recon-all pipeline. Therefore even though the header
information are different, they are still in the same space.

You can convince yourself by using freesurfer's freeview to load both the
MNI template I provide and the MNI template from FSL:

>> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

You should observe they are in perfect alignment (although the values have
been altered by recon-all intensity normalization process). If the
different headers bother you, what you can do is to use freesurfer's
function mri_vol2vol to re-interpolate the volume. For example:

>> mri_vol2vol --mov FSL_MNI152_FreeSurferConformed_1mm.nii.gz --targ
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o
new_volume.nii.gz --no-save-reg

Regards,
Thomas



On Thu, Dec 31, 2015 at 2:59 PM,  wrote:

> Hello Professor Thomas，
>
>
>
> Thank you for your reply so quickly.
>
>
>
> I download the zip files on the webside you gave me, and the images look
> like normal, but when I checked the header information, I found some
> differences with common MNI images.
>
>
>
> Could you see the following pictures and notice the regions with blue
> lines circled.
>
>
>
>
>
>
>
> Excuse me to bother you again.
>
> Best wishes,
>
> Jintao
>
>
>
>
>
>
> *发件人: *Thomas Yeo 
> *发送时间: *2015年12月31日 11:46
> *收件人: *shengjt2...@163.com
> *抄送: *freesurfer 
> *主题: *Re: about functional ROIs
>
>
>
> Hi Jintao,
>
>
>
> This might be a header error in the original files. The error is not
> apparent in the FreeSurfer or FSL environment, but might be problematic
> with mricron (completely my fault).
>
>
>
> Can you try the files from this zip file instead:
> https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation_MICRON.zip
> (courtesy of Chris Rorden).
>
>
>
> Please let me know if this resolves your issues.
>
>
>
> Regards,
>
> Thomas
>
>
>
> On Thu, Dec 31, 2015 at 10:23 AM,  wrote:
>
>
>
> Dear Professor Yeo,
>
>
>
> My name is Sheng Jintao, and I am a master in China.
>
> Recently, I download the ‘Resting State Cortical Parcellation in
> nonlinear MNI152 space’ in
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
> But when I opened images and found they are very stange. Just like this
> sectional drawing. And I don’t know why, therefore, I would love to
> consult you.
>
> Thank you, and I look forward to hearing from you.
>
>
>
> Best wishes,
>
> Jintao
>
>
>
>
>
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms for fMRI.

Topics are flexible. Example topics include individual-subject brain
parcellations, dynamic functional connectivity, meta-analysis, neural
mass modeling, monkey-human homologies, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Doug, the Choi file is a striatal functional connectivity atlas which we
distribute. It's under the average directory.

Hi Bronwyn,

To transform the Choi's striatal atlas to your individual subject, Here's a
(non-ideal) suggestion I previously suggested to another user:

1) Assuming you are quite happy with the freesurfer striatal parcellation
in your individual subjects, then I am assuming freesurfer nonlinear
registration (talairach.m3z) is working quite well. Talairach.m3z warps
your subject to an internal freesurfer space (kinda like MNI305, but not
quite). Let's say the freesurfer recon-all output is at
/SUBJECT_FS/

2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152
1mm template to the internal freesurfer space. Let's say the freesurfer
recon-all output is at /MNI152_FS/

3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest

b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph

This is not optimal because of the double interpolation. You might want to
use the MNI template instead of the Choi_atlas to test the above, so you
can check the goodness of the warp. The final warped MNI template should
hopefully look identical to your subject. If that works, then use the
Choi_atlas. Note that mri_vol2vol does not work properly for
talairach.m3z below
version 5, so you should use version 5x mri_vol2vol.

Regards,

Thomas

On Thu, May 5, 2016 at 10:24 PM, Douglas Greve 
wrote:

>
>
> On 5/4/16 11:40 PM, Bronwyn Overs wrote:
>
> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Yeo 2011 cortical
> parcellations and the Choi 2012 striatal parcellations (7 networks) that
> are provided for download on the freesurfer wiki. My questions are as
> follows:
>
> 1. I noticed that the Yeo 2011 annot files are already available in
> fsaverage/label. How do I map these annot file to each of my subjects so
> that I can extract stats?
>
> Use mri_surf2surf with the --save-annot option
>
> 2. For the Choi 2012 files I wish to use
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do
> I map this file to each of my subjects so that I can extract stats for the
> 7Network parcellation?
>
> I don't know about this file. Where is it? Is it something we distribute?
> doug
>
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
>
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Bronwyn,

Perhaps you can try something like this:

mri_surf2surf --srcsubject fsaverage --trgsubject testsubj --hemi lh --sval-
annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.
annot --tval $SUBJECTS_DIR/testsubj/label/lh.Yeo2011_7Networks_N1000.annot

Regards,
Thomas

On Fri, May 6, 2016 at 11:29 AM, Bronwyn Overs  wrote:

> Hi Doug,
>
> I tried to run the mri_surf2surf command as follows and got this error:
>
> [b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval
> lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval
> lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot
> ERROR: Option --save-annot unknown
> [b.overs~]$
>
> I could not see any --save annot option in the help file. I am running
> this correctly? Should I be suing the .mgz file as the input or is the
> annotation file ok as this is what I want to resample?
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
> On 6/05/2016 12:24 am, Douglas Greve wrote:
>
>
>
> On 5/4/16 11:40 PM, Bronwyn Overs wrote:
>
> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Yeo 2011 cortical
> parcellations and the Choi 2012 striatal parcellations (7 networks) that
> are provided for download on the freesurfer wiki. My questions are as
> follows:
>
> 1. I noticed that the Yeo 2011 annot files are already available in
> fsaverage/label. How do I map these annot file to each of my subjects so
> that I can extract stats?
>
> Use mri_surf2surf with the --save-annot option
>
> 2. For the Choi 2012 files I wish to use
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do
> I map this file to each of my subjects so that I can extract stats for the
> 7Network parcellation?
>
> I don't know about this file. Where is it? Is it something we distribute?
> doug
>
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
>
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Bronwyn,

I was using that as a placeholder. You can use any of these:

Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz

Depending on whether you want the 7 or 17 networks and/or whether you want
to use the loose or tight mask. My suggestion is to use the LooseMask and
then after the parcellation has been project to the subject's native space,
you can mask it again with FreeSurfer's segmentation of striatal regions
(e.g., caudate, putamen and nucleus accumbens) in your subject's native
MRI.

For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you can
use the MNI152 1mm template distributed by FSL.

Regards,
Thomas

On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs  wrote:

> Hi Thomas,
>
> I am not sure which file you are referring to when you say
> "Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
>
> Choi_JNeurophysiol12_MNI152_README
> Choi2012_7Networks_ColorLUT.txt
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>
> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>
> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
> Choi2012_17Networks_ColorLUT.txt
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>
> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>
> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
> FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>
> Which if any of these should I designate as the source in step 3a?
>
> Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this
> correct?
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
> <https://www.facebook.com/NeuroscienceResearchAustralia>[image: Subscribe
> to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe>
> On 6/05/2016 12:50 am, Thomas Yeo wrote:
>
> Hi Doug, the Choi file is a striatal functional connectivity atlas which
> we distribute. It's under the average directory.
>
> Hi Bronwyn,
>
> To transform the Choi's striatal atlas to your individual subject, Here's
> a (non-ideal) suggestion I previously suggested to another user:
>
> 1) Assuming you are quite happy with the freesurfer striatal parcellation
> in your individual subjects, then I am assuming freesurfer nonlinear
> registration (talairach.m3z) is working quite well. Talairach.m3z warps
> your subject to an internal freesurfer space (kinda like MNI305, but not
> quite). Let's say the freesurfer recon-all output is at
> /SUBJECT_FS/
>
> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
> Recon-all will give you a Talairach.m3z that allows you to map the MNI152
> 1mm template to the internal freesurfer space. Let's say the freesurfer
> recon-all output is at /MNI152_FS/
>
> 3) Then do the following:
>
> a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
>
> b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>
> >> setenv SUBJECTS_DIR 
> >> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
> AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
> talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest
> --inv-morph
>
> This is not optimal because of the double interpolation. You might want to
> use the MNI template instead of the Choi_atlas to test the above, so you
> can check the goodness of the warp. The final warped MNI template should
> hopefully look identical to your subject. If that works, then use the
> Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z 
> below
> version 5, so you should use version 5x mri_vol2vol.
>
> Regards,
&

Re: [Freesurfer] cerebellar surface

[Thomas Yeo]

Hi Jim,

You can use mri_tessellate.

Regards,
Thomas

On Mon, May 9, 2016 at 11:11 PM, Alexopoulos, Dimitrios <
alexopoulo...@kids.wustl.edu> wrote:

> Hi all,
>
>
>
> Freesurfer generates a volumetric parcellation of the cerebellum, but is
> there a method to generate the surface reconstruction, or perhaps just a
> hull surface from freesurfer output.
>
>
>
> Jim
>
>
>
>
> The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] cerebellar surface

[Thomas Yeo]

Hi Jim,

Yes. I believe so.

Regards,
Thomas

On Tue, May 10, 2016 at 9:32 PM, Alexopoulos, Dimitrios <
alexopoulo...@kids.wustl.edu> wrote:

> Thanks for the info.
>
>
>
> So the cerebellum surface needs to be generated independently from the
> default cerebral/supratentorial surface generated by recon-all?
>
>
>
> Jim
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Thomas Yeo
> *Sent:* Monday, May 09, 2016 6:20 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] cerebellar surface
>
>
>
> Hi Jim,
>
>
>
> You can use mri_tessellate.
>
>
>
> Regards,
>
> Thomas
>
>
>
> On Mon, May 9, 2016 at 11:11 PM, Alexopoulos, Dimitrios <
> alexopoulo...@kids.wustl.edu> wrote:
>
> Hi all,
>
>
>
> Freesurfer generates a volumetric parcellation of the cerebellum, but is
> there a method to generate the surface reconstruction, or perhaps just a
> hull surface from freesurfer output.
>
>
>
> Jim
>
>
>
>
>
> *The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.*
>
>
> ___
> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> e-mail
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

Hi Bronwyn,

You can first create a striatum mask in the native subject's space:

>> mri_binarize --i subject/mri/aparc+aseg.mgz --match 11 --match 12
--match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz

Then use the resulting mask to mask the striatum parcellation:

>> fslmaths Choi_atlas_AD_subject.nii.gz -mas striatum_mask.nii.gz
Choi_atlas_AD_subject_mask.nii.gz

Regards,
Thomas



On Mon, May 9, 2016 at 11:40 AM, Bronwyn Overs  wrote:

> Hi Thomas,
>
>
> Thanks, I have taken your advise and used the LooseMask for the 7 network
> parcellation in steps 3a and b. How do I now mask it again with
> FreeSurfer's segmentation of striatal regions as you have suggested?
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
> <https://www.facebook.com/NeuroscienceResearchAustralia>[image: Subscribe
> to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe>
> On 9/05/2016 12:29 pm, Thomas Yeo wrote:
>
> Hi Bronwyn,
>
> I was using that as a placeholder. You can use any of these:
>
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>
> Depending on whether you want the 7 or 17 networks and/or whether you want
> to use the loose or tight mask. My suggestion is to use the LooseMask and
> then after the parcellation has been project to the subject's native space,
> you can mask it again with FreeSurfer's segmentation of striatal regions
> (e.g., caudate, putamen and nucleus accumbens) in your subject's native
> MRI.
>
> For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you can
> use the MNI152 1mm template distributed by FSL.
>
> Regards,
> Thomas
>
> On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs 
> wrote:
>
>> Hi Thomas,
>>
>> I am not sure which file you are referring to when you say
>> "Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
>>
>> Choi_JNeurophysiol12_MNI152_README
>> Choi2012_7Networks_ColorLUT.txt
>> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>>
>> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>>
>> Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>> Choi2012_17Networks_ColorLUT.txt
>> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>>
>> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>>
>> Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
>> FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>>
>> Which if any of these should I designate as the source in step 3a?
>>
>> Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this
>> correct?
>>
>> Kind regards,
>>
>> Bronwyn Overs
>> Research Assistant
>> [image: Neuroscience Research Australia]
>>
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> *M* 0411 308 769 *T* +61 2 9399 1883 <%2B61%202%209399%201883>
>> neura.edu.au
>>
>> [image: Follow @neuraustralia on twitter]
>> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
>> <https://www.facebook.com/NeuroscienceResearchAustralia>[image:
>> Subscribe to the NeuRA Magazine]
>> <http://www.neura.edu.au/help-research/subscribe>
>> On 6/05/2016 12:50 am, Thomas Yeo wrote:
>>
>> Hi Doug, the Choi file is a striatal functional connectivity atlas which
>> we distribute. It's under the average directory.
>>
>> Hi Bronwyn,
>>
>> To transform the Choi's striatal atlas to your individual subject, Here's
>> a (non-ideal) suggestion I previously suggested to another user:
>>
>> 1) Assuming you are quite happy with the freesurfer striatal parcellation
>> in your individual subjects, then

Re: [Freesurfer] Question on Yeo 2015 cognitive atlas

[Thomas Yeo]

Hi Josh,

Thanks for your interest. The networks are in MNI152 space. My
understanding is that you want to map the networks onto the structural
T1 data of your subjects. Here's my suggestion on how to do it:

1) Assuming you are quite happy with the freesurfer recon-all of your
individual subjects, then this means that freesurfer nonlinear
(volumetric) registration (talairach.m3z) is working quite well.
Talairach.m3z warps your subject to an internal freesurfer space
(kinda like MNI305, but not quite). Let's say the freesurfer recon-all
output is at /SUBJECT_FS/

2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the
MNI152 1mm template to the internal freesurfer space. Let's say the
freesurfer recon-all output is at /MNI152_FS/

3) Then do the following:

a) First sample C1-C12 (Yeo_components2mm.nii.gz) to norm.mgz of
MNI152_FS (because C1-C12 are 2mm, but norm.mgz is 1mm isotropic):

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov Yeo_components2mm.nii.gz --s MNI152_FS --targ 
>> /MNI152_FS/mri/norm.mgz --regheader --o Yeo_components1mm.nii.gz

b) Warp the Yeo_components1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov Yeo_components1mm.nii.gz --s MNI152_FS --targ 
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
>> Yeo_components_internal_space.nii.gz

c) Warp Yeo_components_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS 
>> --targ Yeo_components_internal_space.nii.gz --m3z talairach.m3z --o 
>> Yeo_components_subject_space.nii.gz --interp nearest --inv-morph

This is not optimal because of the multiple interpolation, but the
networks are quite smooth anyway, so it should be ok.

You might want to use the FSL MNI152 2mm template instead of
Yeo_components2mm.nii.gz to test the steps above, so you can check the
goodness of the warp. The final warped MNI template should hopefully
look identical to your subject. If that works, then use
Yeo_components2mm.nii.gz. Note that mri_vol2vol does not work properly
for talairach.m3z below version 5, so you should use version 5x
mri_vol2vol.

Regards,
Thomas

On Wed, May 18, 2016 at 3:53 AM, Josh Gray  wrote:
> Hello,
>
> I am interested in applying the Yeo 2015 cognitive atlas to structural data.
> Basically, I want to quantify networks C1-12 in my structural data by
> exporting the voxel size of each network for each subject into an text file
> (so I would have left and right hemisphere voxel totals for networks C1-12
> for each subject). It is analogous to what is routinely done with the
> desikan and destrieux atlas. I know you can change the threshold of the
> networks, but I suspect 1e-5 is fine (i.e., what is depicted on the
> website). Is there a quick way to do this?
>
> Thank you,
> Josh Gray
>
> --
> Graduate Student
> Psychology Dept. - Clinical Program
> Experimental & Clinical Psychopharmacology Laboratory
> University of Georgia
>
> ___
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Re: [Freesurfer] Merging PArcellation labels

[Thomas Yeo]

Hi Anupa,

In addition to the Desikan and Destrieux parcellations, FreeSurfer 5.2
also include other cortical parcellations
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes).

In particular, the resting-state parcellation or Mindboggle atlas
might be relevant to you if you are interested in the frontal cortex.

Cheers,
Thomas

On Mon, Mar 25, 2013 at 11:31 PM, Laura M. Tully
 wrote:
> it sounds like you want a different parcellation of the lateral prefrontal
> cortex than what is offered by the default atlas (aparc, AKA the desikan
> atlas) - I suggest you load in ?h.aparc.a2009s.annot (aka the destrieux
> atlas) as your annotation in tksurfer and select the annotations of the PFC
> that you want from there and save as labels. The aparc.a2009 annotation
> offers a more fine grained parcellation of the PFC - e.g. you can get the
> DLPFC by merging the middle frontal gyrus & middle frontal sulcus
> parcellations.
>
>
> On Mon, Mar 25, 2013 at 3:19 AM, Anupa AV  wrote:
>>
>> Dear Laura,
>> Thank you so much.
>> It worked well.
>> Do you know how to make cuts on the merged label, for eg. if I need to
>> seperate DLPFC from premotor cortex.
>>
>>
>> 
>> From: Laura M. Tully 
>> To: Anupa AV 
>> Cc: "freesurfer@nmr.mgh.harvard.edu" 
>> Sent: Sunday, March 24, 2013 12:20 AM
>> Subject: Re: [Freesurfer] Merging PArcellation labels
>>
>> First save each parcellation that you want as its own separate label by
>> selecting it in tksurfer (simply click on it with  your mouse and its
>> boarder will be highlighted in yellow) and then file -> label -> save
>> selected label...  Then you can merge these separate labels into one label
>> at the command line using mri_mergelabels -i [labelfile1] -i [labelfile2] -o
>> [newlabelfile.label]
>>
>> If doing glms from the command line you can then feed mri_glmfit the label
>> with the --label option. This will conduct the glm in the region specified
>> in the label only (i.e. an roi analysis)
>>
>> There is also a quick way to turn all of the desikan parcellations into
>> individual label files at the command line using mri_annotation2label I
>> think, but I can't remember precisely. This is a lot faster than using
>> tksurfer as it simply dumps all the individual parcellations into a
>> specified output directory. But I don't know if you can do it with the
>> Destrieux atlas parcellations (if you were interested in doing that.)
>>
>> Laura.
>>
>>
>>
>>
>>
>> On Sat, Mar 23, 2013 at 2:36 AM, Anupa AV  wrote:
>>
>> Dear All,
>>
>> Can anyone tell me how to merge the parcellation labels using tksurfer.?
>> For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and
>> caudal middle frontal gyrus.
>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>> --
>> Laura M. Tully, MA
>> Social Neuroscience & Psychopathology, Harvard University
>> Center for the Assessment and Prevention of Prodromal States, UCLA Semel
>> Institute of Neuroscience
>> ltu...@mednet.ucla.edu
>> ltu...@fas.harvard.edu
>> 310-267-0170
>> --
>> My musings as a young clinical scientist:
>> http://theclinicalbrain.blogspot.com/
>> Follow me on Twitter: @tully_laura
>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
>
> --
> --
> Laura M. Tully, MA
> Social Neuroscience & Psychopathology, Harvard University
> Center for the Assessment and Prevention of Prodromal States, UCLA Semel
> Institute of Neuroscience
> ltu...@mednet.ucla.edu
> ltu...@fas.harvard.edu
> 310-267-0170
> --
> My musings as a young clinical scientist:
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
>
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>
> The informati

Re: [Freesurfer] How to get surface-based AAL template

[Thomas Yeo]

Hi Zhi Liang,

Out of curiosity, why not just use the FreeSurfer parcellations, so
you don't end up with holes in the sulci/gyri?

--Thomas

On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk
 wrote:
> I faced this problem a while ago. Both MNI to fsaverage, MNI itself and
> Colin27 didn’t work sufficiently for sampling the labels, all had problems
> with the registration causing holes in the sulci and gyri ending up in the
> wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but
> might also be bad, since you often don’t want to look at an in complete
> label). I ended up making my own gcs fom a training set with mris_ca_train.
> Now I can segment surfaces just by calling mris_ca_label which works
> flawlessly and consistent throughout subjects.
>
>
>
> Best,
>
> Martijn
>
>
>
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens ZhiLiangLong
> Verzonden: zaterdag 30 maart 2013 16:25
> Aan: Garikoitz Lerma-Usabiaga
> CC: Freesurfer
> Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
>
>
>
> Dear Gari:
>
> Thank you for give me suggestions patiently. i figured it out as you
> suggested. it works well. I have one more question: Do you know there are
> published papers which use the surface-based aal template (or something like
> this) to do research (e.g. cortical network analysis based on this
> template)?
>
>
>
> Best wishes.
>
> zhiliang
>
> At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" 
> wrote:
>
> Hi Zhiliang,
>
> 1- well, I just recon-all-ed their subject again with the newest version.
> Recon-all -s Colin -all
>
> 2- maybe Doug or some other will answer this question better. I don't know
> the exact differences between fs mni305 and fs mnicolin27. What I know is
> that going the fsaverage path I couldn't obtain reliable transformations of
> the AAL labels. I think this was because fsaverage is very smoothed.
> Spm_register and vol2surf weren't working well.
>
>
>
> The thing is, for group analysis, you can use Colin (or any other), as I
> understood it. When you use -qcache your data goes to fsaverage, but you can
> do it manually and specify that you want Colin instead (maybe someone can
> confirm it). If you are going to use just the AAL average CTs, then you just
> need to use surf2surf or label2label and you won't need fsaverage at all.
>
>
>
> 3- well, the spm single subject and Colin from Surfrend are the same subject
> but not exactly the same image. You do bbregister to them and obtain your
> register.dat matrix (you name it), and it goes from 2mm to 1mm and has some
> minimal translation. If you see both T1-s with tkregister you will see that
> they are almost the same (the spm version a little bit blurred, because of
> the resolution). You use this register.dat when doing vol2surf of the
> AAL.nii to your AAL.mgh surface ROI.
>
>
>
> Hope this helps!
>
> Gari
>
>
> On 27/03/2013, at 14:06, ZhiLiangLong  wrote:
>
> Dear Br:
>
>Thanks for your help. I have downloaded Colin 27 subject, and the
> Surfrend toolbox. But I still have some questions about the process.
>
>1. You said I need transform the Colin 27 to the latest FS version
> (v.5.2). But i don't know how to do this. It is helpful if you can provide
> some information.
>
>   2. How does the Colin 27 space differs from fsaverage MNI305 space? The
> group analysis of cortical thickness is conducted in fsaverage space, after
> importing AAL ROI into Colin 27 space, should i  transform the obtained ROI
> into fsaverage space?
>
>  3. i don't understand what is the register.dat between COlin 27 and SPM-s
> single subject t1.nii used for? I have tried the Surfrend, and found there
> was no entry for input of register file during the processing.
>
>
> Looking forward to your reply.
>
> Best wishes.
>
>
> zhiliang
>
>
> At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" 
> wrote:
>
> Hi,
>
> In my case transformation to fsaverage did not work very well. What I did
> was:
>
> -  from Surfrend page download Colin 27 subject and transform it to the
> latest version (now 5.2)
>
> - with bbregister obtain register.dat between this Colin 27 subject and
> SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are
> defined in Colin 27. As they are the same subject, the registering is very
> good.
>
> - now you can import every AAL ROI (in .nii form) to an annotation or in the
> form of individual labels to your FS Colin 27, using the newly created
> registering file.
>
> - now you can use surf2surf or label2label to go to your subjects and obtain
> stats.
>
>
>
> Br!
>
>
> On 27/03/2013, at 05:35, ZhiLiangLong  wrote:
>
> Hi all;
>
>   I need a suface-based aal template which is compatible with FS surface
> file. Is there a way i can get the surface-based aal template? I have an
> idea, that is to just transform the AAL template (.nii file) in MNI space
> onto the surface template (e.g. fsaverage template) in FS. Is it correct? if
>

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis

[Thomas Yeo]

Hi Ludovico,

The mri_vol2surf example I sent you directly resample to fsaverage5,
which is around 4mm spacing, resulting in 18715 vertices for both
hemispheres combined after excluding the medial wall in the surfaces.

I am also including the freesurfer mailing list in the email as
suggested by Bruce.

--Thomas

On Thu, May 16, 2013 at 8:25 PM, Bruce Fischl
 wrote:
> Hi Ludovico
>
> I wouldn't downsample before calling mri_surf2surf. We have tools for
> uniformly parcellating the cortex (mris_make_face_parcellation) that can be
> used for this purpose after sampling the timecourses to the cortex.
>
>
> cheers
> Bruce
> On Thu, 16 May 2013, Ludovico Minati wrote:
>
>> Hi Bruce,
>>
>> many thanks. Yes sorry I shall use the list from now on. But let me
>> just ask you a clarification as we are already on these questions
>>
>> For our connectivity analyses, at present we parcellated in 3D volume
>> space the cortex into a pre-set number of roughly equal volume
>> parcels, ranging in number between around 500 to 10,000. I would need
>> to translate this approach to the surface space in Freesurfer, i.e. be
>> able to smooth on the cortical surface and undersample it. What is the
>> best approach that can be used?
>>
>> Along this like: you wrote around 150k vertices/hemisphere. For our
>> purposes that's an enormous number, much larger than the number of EPI
>> voxels. How can we mesh downsample before calling mri_vol2surf?
>>
>> Again thanks for your kind help and patience
>>
>> Ludovico
>>
>>
>> On 16 May 2013 14:09, Bruce Fischl  wrote:
>>>
>>> Hi Ludovico
>>>
>>> can we move this discussion to the FreeSurfer list in the future so
>>> others
>>> can answer?
>>>
>>> 1. Hard to say as sometimes one works better than the other, you'll just
>>> have to try. The transform should be rigid (6DOF) since the scalings are
>>> read from the header, why would you want affine? I think Doug has worked
>>> on
>>> this and you can specify it in the bbregister command line, but I've
>>> never
>>> used it.
>>>
>>> 2. About 150K vertices/hemisphere. They are distributed initially at 1mm
>>> spacing (the surface of the voxels), and cannot be tuned. There are some
>>> tools around for mesh downsampling if you want, and this is even easier
>>> if
>>> you go to fsaverage space (with mri_surf2surf) where we have
>>> representations
>>> based on recursive icosahedral supersamplings.
>>>
>>> 3.  This is due to a bug in the initial nifti format that didn't allow
>>> any
>>> one dimension greater than 64K. If you output in .mgz it should be
>>> nvertices
>>> x 1 x 1 x ntimepoints.
>>>
>>> 4. Search for "coordinate systems" on our wiki. This is documented
>>> extensively.
>>>
>>> there are also matlab i/o functions for reading/writing all our formats
>>> (e.g. MRIread.m)
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 16 May 2013, Ludovico Minati wrote:
>>>
>>>> Hi Thomas,
>>>>
>>>> thanks. A few quick questions, which hopefully will take little of
>>>> your time but save me a lot of hassle:
>>>>
>>>> 1) bbregister. Do you advise using FLIRT or SPM for initialization? Is
>>>> this a rigid-body transformation, or an affine one? Any way I can
>>>> control the DOF? If I use SPM shall I feed the mean realigned volume
>>>> here, as I expect?
>>>>
>>>> 2) recon-all. What is the typical number of vertices for the cortex?
>>>> Any way I can control it, i.e. sample more or less finely? This would
>>>> be particularly relevant for our task.
>>>>
>>>> 3) mri_vol2surf. Perhaps naively I was expecting an output file simply
>>>> consisting of a list of values, i.e. one per vertex (assuming a single
>>>> input volume that is). But the documentation says: "The output will be
>>>> a data set with Nv/R colums, 1 row, R slices, and Nf frames..." What
>>>> is the reshaping factor R for? How do I deal with this, i.e. how do I
>>>> simply get a value per vertex? Or am I missing something here? Is
>>>> mri_vol2surf averaging over neighbouring vertices?
>>>>
>>>> 4) Where do I read the Euclinean co-ordinates of the vertices from?
>>>>
>>>> Cheers
>>>>
>>>> Ludovico
>>&g

Re: [Freesurfer] log transform of the mgh file

[Thomas Yeo]

you can probably use  fscalc.fsl. Type "fscalc.fsl --help" for more information.

--Thomas

On Thu, May 23, 2013 at 9:26 AM, Minjie Wu  wrote:
> Hello All,
>
> Is there any way in FreeSurfer to take the log transform of a .mgh file and 
> save the output as .mgh file?
>
> Thank you.
>
> Minjie
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Re: [Freesurfer] freesurfer 5.2 mac download link

[Thomas Yeo]

Hi Jonathan,

There are problems with FreeSurfer 5.2, so you should probably
download FreeSurfer 5.3 instead.

Cheers,
Thomas

On Fri, May 24, 2013 at 5:51 AM, Jonathan Holt  wrote:
> can't seem to find it, would appreciate a link!
>
> jon
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Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis

[Thomas Yeo]

Hi Doug and Bruce,

Doug's comment about vertex spacing and its dependence on the surface
of choice has gotten me thinking:

When I smooth my fMRI data using 6mm kernel, I use the command
"mri_surf2surf --hemi lh --s fsaverage6 --sval lh.fmri.nii.gz --cortex
--fwhm-trg 6 --tval rh.fmri.nii.gz --reshape".

Which surface is "6mm" defined on? Is it .sphere, .white, or something
else? If ".sphere", do you scale the sphere so the surface area is
equal to some value?

Thanks,
Thomas


On Thu, May 16, 2013 at 11:48 PM, Douglas N Greve
 wrote:
> Hi Ludovico, I'm not sure exactly what your pipeline is, but you should use 
> fsaverage for vol2surf, then go from fsaverage to fsaverage4 or 5 with 
> mri_surf2surf. The reason is that if you go directly to 4 or 5, you will miss 
> data between the vertices. The distance between the vertices for fsaverage4 
> is about 5.5mm and it is about 3mm for fsaverage5, 1.4 for fsaverage6, and 
> .7mm for fsaverage (these are all for the white surface).
>
> doug
>
> On 05/16/2013 08:58 AM, Bruce Fischl wrote:
>> you would change fsaverage5 to fsaverage4 (fewer vertices) or fsaverage6
>> (more vertices)
>> On Thu, 16 May 2013, Ludovico Minati wrote:
>>
>>> Hi Thomas
>>>
>>> many thanks. So, in the example you have sent me, how should I go
>>> about if I wished to vary the granularity?  Are there different meshes
>>> to reshape or should I generate them somehow?
>>>
>>> Ludovico
>>>
>>>
>>> On 16 May 2013 14:47, Thomas Yeo  wrote:
>>>> Hi Ludovico,
>>>>
>>>> The mri_vol2surf example I sent you directly resample to fsaverage5,
>>>> which is around 4mm spacing, resulting in 18715 vertices for both
>>>> hemispheres combined after excluding the medial wall in the surfaces.
>>>>
>>>> I am also including the freesurfer mailing list in the email as
>>>> suggested by Bruce.
>>>>
>>>> --Thomas
>>>>
>>>> On Thu, May 16, 2013 at 8:25 PM, Bruce Fischl
>>>>  wrote:
>>>>> Hi Ludovico
>>>>>
>>>>> I wouldn't downsample before calling mri_surf2surf. We have tools for
>>>>> uniformly parcellating the cortex (mris_make_face_parcellation) that can 
>>>>> be
>>>>> used for this purpose after sampling the timecourses to the cortex.
>>>>>
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>> On Thu, 16 May 2013, Ludovico Minati wrote:
>>>>>
>>>>>> Hi Bruce,
>>>>>>
>>>>>> many thanks. Yes sorry I shall use the list from now on. But let me
>>>>>> just ask you a clarification as we are already on these questions
>>>>>>
>>>>>> For our connectivity analyses, at present we parcellated in 3D volume
>>>>>> space the cortex into a pre-set number of roughly equal volume
>>>>>> parcels, ranging in number between around 500 to 10,000. I would need
>>>>>> to translate this approach to the surface space in Freesurfer, i.e. be
>>>>>> able to smooth on the cortical surface and undersample it. What is the
>>>>>> best approach that can be used?
>>>>>>
>>>>>> Along this like: you wrote around 150k vertices/hemisphere. For our
>>>>>> purposes that's an enormous number, much larger than the number of EPI
>>>>>> voxels. How can we mesh downsample before calling mri_vol2surf?
>>>>>>
>>>>>> Again thanks for your kind help and patience
>>>>>>
>>>>>> Ludovico
>>>>>>
>>>>>>
>>>>>> On 16 May 2013 14:09, Bruce Fischl  wrote:
>>>>>>> Hi Ludovico
>>>>>>>
>>>>>>> can we move this discussion to the FreeSurfer list in the future so
>>>>>>> others
>>>>>>> can answer?
>>>>>>>
>>>>>>> 1. Hard to say as sometimes one works better than the other, you'll just
>>>>>>> have to try. The transform should be rigid (6DOF) since the scalings are
>>>>>>> read from the header, why would you want affine? I think Doug has worked
>>>>>>> on
>>>>>>> this and you can specify it in the bbregister command line, but I've
>>>>>>> never
>>>>>>> used it.
>>>>>>>
>>>

Re: [Freesurfer] integrating another atlas into Freesurfer

[Thomas Yeo]

Hi Jeff,

If you run recon-all on your individual subjects, it would have
automatically generate the registration files (?h.sphere.reg) to fsaverage.
Doug's reply about mri_surf2surf should work. You just need to apply
mri_surf2surf separately for the left and right annots.

Cheers,
Thomas


On Sun, Jul 14, 2013 at 10:27 PM, Jeff Eriksen  wrote:

> Bruse,
>
> I apologize, I thought you were answering another question that I had
> submitted, which I had foremost in my mind. I will look at mri_label2label
> in more detail now in the proper context.
>
> Thanks,
> -Jeff
>
> On 7/13/13 11:31 AM, "Bruce Fischl"  wrote:
>
> >Hi Jeff
> >mri_label2label should do what you want
> >Cheers
> >Bruce
> >
> >On Jul 12, 2013, at 6:45 PM, Jeff Eriksen  wrote:
> >
> >> I have the Yeo resting-state fMRI atlases which I downloaded from
> >>
> >> http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011
> >>
> >> They consist of 3 versions, fsaverage being of interest here. The
> >> fsaverage folder provided includes the typical FS folders corresponding
> >>a
> >> recon-all for the average brain for this atlas. I wish to use this high
> >> resolution atlas to parcellate my individual subjects. I am unclear how
> >>to
> >> go about this. I have perused wiki pages on
> >>
> >> Annotation files
> >> FS labels
> >> Automatic surface labeling process
> >> Surface registration process
> >>
> >> but still do not find a clear path to my goal. Specifically I would like
> >> to end up with a matching set of surface and annot files, as high of
> >> resolution as possible, for each of my subjects. Using some specific
> >> numbers, the Yeo atlas has around 300,000 vertices when combining the
> >> lh.pial and rh.pial surfaces. The matching annot files I believe are
> >> l&rh.Yeo2011_17Networks_N1000.annot, which together should also have
> >> 300,000 vertices. I suppose what I need to do is align each of my
> >>subjects
> >> to this atlas and project the atlas onto each subject to get a new
> >>surface
> >> and annot file for that subject, which will have some unique number of
> >> vertices for each subject.
> >>
> >> Please point me to the right set of documentation that will tell me how
> >>to
> >> do this. Thanks,
> >>
> >> -Jeff
> >>
> >>
> >> ___
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> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >
> >
> >The information in this e-mail is intended only for the person to whom it
> >is
> >addressed. If you believe this e-mail was sent to you in error and the
> >e-mail
> >contains patient information, please contact the Partners Compliance
> >HelpLine at
> >http://www.partners.org/complianceline . If the e-mail was sent to you in
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> >but does not contain patient information, please contact the sender and
> >properly
> >dispose of the e-mail.
> >
>
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Re: [Freesurfer] break up time course nifti (fwd)

[Thomas Yeo]

fslsplit is another option.

--Thomas


On Tue, Jul 30, 2013 at 7:11 AM, MCLAREN, Donald
wrote:

> I'd convert them to nifti files and then use SPM. SPM won't know the
> difference between a surface nifti and a volume nifti.
>
> Best Regards, Donald McLaren
> =
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital
> and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
> =
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> On Mon, Jul 29, 2013 at 6:37 PM, Louis Nicholas Vinke
>  wrote:
> > Forwarding to the list so others can chime in.
> >
> > -- Forwarded message --
> > Date: Mon, 29 Jul 2013 18:19:38 -0400
> > From: Subhabrata Chaudhury 
> > To: Louis Nicholas Vinke ,
> > Aaron Tanenbaum 
> > Subject: Re: [Freesurfer] break up time course nifti
> >
> > Greetings Dr. Vinke and Dr. Tanenbaum,
> > I saw your recent freesurfer posts.
> > I have piped BOLD volumeetric nii files for each TR onto the subject's
> > freesurfer surface using
> > bbregister. The resulting surface files (1 for each TR) are in mgh
> format.
> > Now I want to do a first
> > level glm analysis on the surface files.
> > I havent come across any tool that will allow me to conduct a first level
> > glm analysis using the
> > mgh files. So I was thinking if there is a way to convert these mgh
> files to
> > nii files and then be
> > able to read in these 'surface' nii files into fsl or spm or afni.
> > Do you have some experience in this regard that you can share ?
> > I will be highly obliged if you can help me with this and share your
> > thoughts.
> >
> > Thank you for your help,
> >
> > Subha
> >
> >
> >
> >   - Original Message -
> >
> >   From: Louis Nicholas Vinke
> >
> >   Sent: 07/29/13 05:46 PM
> >
> >   To: Aaron Tanenbaum
> >
> >   Subject: Re: [Freesurfer] break up time course nifti
> >
> >
> >
> >
> > Hi Aaron, You can use the -f or -nth flags with mri_convert. -Louis
> >
> > On Mon, 29 Jul 2013, Aaron Tanenbaum wrote:
> >
> >> hola freesurfers, I have a time course surface nii files. I would like
> to
> >> break up the time course into many nii files for each time frame. Is
> there
> >> an easy way of doing this. Thank you Aaron Tanenbaum
> >>
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Re: [Freesurfer] Cerebellar parcellation

[Thomas Yeo]

Hi Charles,

The new cortical/cerebellar/striatum parcellations are derived from the
resting-state fMRI data averaged across 1000 subjects in MNI152 space.

If your subjects have already been warped to MNI152 space, then you can
simply use those parcellations (which are in the $FREESURFER_HOME/average/
directory). Alternatively, you could warp the MNI152 parcellations to your
subjects' native structural MRI space.

I am not sure if Bruce has a better solution since he says "we are working
on something" in this email to you.

Regards,
Thomas


On Wed, Jul 31, 2013 at 5:23 AM, charles laidi wrote:

> Dear Freesurfers,
>
> I would like to perform cerebellar parcellation on structural mri with
> freesurfer. I asked if this was possible 6 months ago (see message below,
> saying that this feature wasn't available for now).
> I checked on freesurfer wiki the release notes about Freesurfer version
> 5.2.0 saying that new cortical parcellations and label were available.
>
> "Cortical, Cerebellar, Striatum Parcellation in MNI152 space found in
> average/,
> average/ and
> average/. See README file in each directory
> for more details. Note that these README files will be updated to reflect
> minor improvements in parcellations beyond the publication wikipages".
>
> My understanding is that cerebellar parcellation on structural mri is
> still not available, could you tell me if I'm right ?
> When I'm checking the link on the release notes it doesn't seems to
> concern structural imaging.
>
> Thanks a lot for your attention, sorry if my question seems obvious but
> I'm not very familiar with freesurfer.
>
> Charles
>
>
> PS :
> -answer :
> Hi Charles,
> that is true at the moment, although we are working on something that
> should be ready relatively soon.
>
> cheers
> Bruce
>
> -question :
> Dear freesurfer,
> I'm trying to perform parcellation on the cerebellum. After reading
> closely freesurfer wiki and the questions related to this topic on the
> mailing list, my understanding is that there is no way to perform fully
> automted cerebellar parcellation on structural mri with freesurfer.
> Could you tell me if I'm right ?
>
> Thanks a lot for your attention
>
> Charles
>
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Re: [Freesurfer] TALx coordinates

[Thomas Yeo]

Hi Gari,

The transformation actually consists of a 3 x 3 matrix and a 3 x 1
translation vector. The use of a 4 x 4 matrix allows the
representation of an affine transformation as a matrix multiplication
(http://en.wikipedia.org/wiki/Affine_transformation#Representation).

--Thomas

On Wed, Sep 11, 2013 at 4:21 PM, Garikoitz Lerma-Usabiaga
 wrote:
> Hi Doug,
> just a very naive question about coordinate change: why do we need the
> fourth component? I mean, shouldn't be the transformation matrix 3x3 instead
> of 4x4 for a coordinate change in 3D space?
> thanks!
> Gari
>
>
> On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve
>  wrote:
>>
>> Hi Yang, I've computed a matrix that should do the trick. If you are in
>> matlab, then
>>
>> M = [0.9975   -0.00730.0176   -0.0429
>>  0.01461.0009   -0.00241.5496
>> -0.0130   -0.00930.99711.1840
>>   0 0 01.]
>> P305 = [MNI305x MNI305y MNI305z 1]';
>> P152 = M*P305
>>
>> Can you give this a shot and see if it makes sense? It will probably be
>> hard to tell since the matrix is pretty close to identity.
>>
>> doug
>>
>>
>>
>>
>> On 09/10/2013 05:17 PM, Yang, Daniel wrote:
>> > Thanks, Doug. I am really hoping to get MNI152 (because I also use
>> > fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152
>> > coordinates?
>> >
>> > Best,
>> > Daniel
>> >
>> > --
>> > Yung-Jui "Daniel" Yang, PhD
>> > Postdoctoral Researcher
>> > Yale Child Study Center
>> > New Haven, CT
>> > (203) 737-5454
>> >
>> > On 9/10/13 5:14 PM, "Douglas N Greve" > > > wrote:
>> >
>> >
>> > It is an estimate of Tal coords from the MNI305. See
>> >
>> > http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
>> >
>> > If you want MNI305, run mri_surfcluster with --nofixmni
>> >
>> > doug
>> >
>> >
>> >
>> > On 09/10/2013 05:08 PM, Yang, Daniel wrote:
>> >
>> > Hi all,
>> >
>> > The output of mri_surfcluster --sum shows TalX TalY TalZ. I am
>> > wondering if they are based on the Talairach system or some
>> > sort of
>> > MNI-Talairach system. If the latter, can you tell me something
>> > more
>> > about it? Like a webpage that describes its relationship
>> > between the
>> > MNI152 or the Talairach system?
>> >
>> > I find it confusing because mri_surfcluster said: "INFO:
>> > fixing MNI
>> > talairach coordinates"
>> >
>> > Thanks!
>> > Daniel
>> >
>> > --
>> > Yung-Jui "Daniel" Yang, PhD
>> > Postdoctoral Researcher
>> > Yale Child Study Center
>> > New Haven, CT
>> > (203) 737-5454
>> >
>> >
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu 
>> > Phone Number: 617-724-2358
>> > Fax: 617-726-7422
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > Outgoing:
>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >
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>> > The information in this e-mail is intended only for the person to
>> > whom it is
>> > addressed. If you believe this e-mail was sent to you in error and
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>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>>
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Re: [Freesurfer] mapping extracted MNI152 ROIs to individual subjects

[Thomas Yeo]

Hi Paul,

What we typically do is to either (1) Transform the subjects' fMRI
data to MNI152 space and then use the MNI ROIs to perform the
functional connectivity analysis OR (2) Transform the subjects' fMRI
data to fsaverage surface space and then use the surface-based
fsaverage ROIs to perform the functional connectivity analysis. The
second approach is definitely more accurate because the ROIs were
originally generated in fsaverage space and then projected to MNI152
space and because working on the surface respects the cerebral
cortex's 2D topology.

If for some reason, you really want to perform the analysis in the
subjects' native space, I would suggest resampling the surface-based
fsaverage ROIs (instead of the MNI152 ROIs) to your subject's native
space . Assuming you have run your subject's anatomical through
recon-all, I believe (and someone please correct me if I am wrong) you
can use mri_label2vol to do the resampling.

--Thomas

On Sat, Sep 14, 2013 at 4:19 AM, Paul Beach  wrote:
> Hello Freesurfer experts,
>
> I am currently trying to take extracted cortical networks from the
> Yeo_JNeurophysiol11_MNI152 package and translate them to individual subjects
> to perform functional connectivity analyses - based on the individual
> networks, themselves. Currently the extracted ROIs are in '.nii.gz' format.
>
> My question is: How do I take the extracted ROIs and map them on to
> individual subjects? My thought was that mri_vol2vol could perhaps
> accomplish this, but I cannot find a help file for this command that would
> guide me in developing the line of code to write.
>
>
> Thanks!
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
>- Bozoki Lab: Neurology/Radiology
>
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Re: [Freesurfer] Flipped and non-flipped data

[Thomas Yeo]

To add on to Bruce's explanation, the freesurfer parcellation atlas
(which for example specifies the probability of precentral gyrus at a
particular location) is not symmetric, thus it will treat the left and
right hemispheres of your subject differently if you flipped it.

--Thomas

On Sun, Jun 17, 2012 at 10:04 PM, Bruce Fischl
 wrote:
> Hi Remmelt
>
> folding patterns are not symmetric across the hemispheres, so the cortical
> parcellation will change if you flip things left/right, which is
> appropriate. I would be surprised if you see much change in the thickness
> though.
>
> cheers
> Bruce
>
>
>
>
> On Fri, 15 Jun 2012, Schur, Remmelt R. wrote:
>
>> Dear Freesurfers,
>>
>> Grey matter volumes of the same structure seem to be measured differently
>
> depending on if FreeSurfer establishes it as in the left or in the right
> hemisphere. For example, if I take a look at the caudal anterior cingulate
> in the right hemisphere and I flip the image (creating a mirror image of the
> same hemisphere, which will then be treated by FreeSurfer as a left
> hemisphere), the same structure has a totally different grey matter volume
> (see attachment, on the right the original and on the left the flipped
> version). Does anybody know what's the logic behind this and what's the best
> way to avoid FreeSurfer creating asymmetry between left and right hemisphere
> (maybe averaging flipped and non-flipped data?)
>>
>>
>> Thanks!
>>
>> Kind regards,
>> Remmelt Schür
>>
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Re: [Freesurfer] Fwd: LGI using Yeo Atlas

[Thomas Yeo]

Hi Martin,

Sorry for the slow reply. Antonin is right about the mri_segstats.

To map the surface parcellation from fsaverage to your individual
subject's anatomical space, you can do the following:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh 
>> --sval-annot lh.Yeo2011_17Networks_N1000.annot  --tval 
>> $SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot

# Transform from subject's surface into your subject's volume (I am
not super sure about this. You probably want to double check the
output is correct)
>> mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot --o 
>> outfile.nii.gz --hemi lh --subject HS_001 --regheader

Regards,
Thomas

On Sat, Feb 11, 2017 at 5:01 AM, Antonin Skoch  wrote:
> Dear Martin,
>
> I think that this thread is relevant for you:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34508.html
>
> You would have to map Yeo atlas to individual brain and then extract the LGI
> values using command:
>
> mri_segstats --annot my_subject_id lh aparc --i
> $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
>
> where aparc replace by name of your generated Yeo atlas annot file.
>
> Regards,
>
> Antonin Skoch
>
>
> Hi everyone,
>
> I was wondering if someone could please address the following question
> regarding FreeSurfer usage.
>
> I would really appreciate any help.
>
> Thanks.
>
> Hi,
>
> I used following command to extract LGI values from a set of subjects:
>
> recon-all -s  -localGI
>
> Output stats is saved in lh.aparc_lgi.stats file. By default, its
> calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am
> interested in calculating LGI values using Yeo atlas of 7 networks. I was
> wondering how can I change the default atlas to Yeo atlas to get LGI value
> for each subject.
>
> Thanks a lot.
>
>
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Re: [Freesurfer] Cortical Parcellations in individual space using Yeo et al 2011

[Thomas Yeo]

Hi Emma,

I recommend that you follow the mri_surf2surf and mri_label2vol route.
As recommended in the other emails, you should probably load the
resulting parcellations and make sure they look ok.

As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so
applicable here because they require multiple subjects with
resting-state parcellations in order to train the classifier. We are
working on an individual subject 7-network and 17-network parcellation
algorithm, but it's not ready yet.

What kind of edits have you already done? If your edits involve
correcting the gray/white matter segmentation and the cortical
surfaces, then your edits should be reflected (since mri_surf2surf and
mri_label2vol should utilized the updated cortical surfaces). However,
if your edits involving editing the Desikan's parcellation itself,
then probably not.

Regards,
Thomas

On Wed, Feb 15, 2017 at 6:11 AM, Bailin, Emma
 wrote:
> Hello,
>
>
>
> I’m preparing to do resting state analyses and I’d like to use the Yeo 2011
> network atlas for the cortical parcellations. Looking through the archive, I
> know that mri_surf2surf with the –sval-annot flag can be used to convert the
> fsaverage from the Yeo et al 2011 study to an individual subject space, but
> I noticed a caveat to this when I called mri_surf2surf –help. The caveat is
> on example 5: “this is not a substitute for running the cortical
> parcellation! The parcellations that it maps to the new subject may not be
> appropriate for that subject.”
>
>
>
> Given this information, I’ve got a few questions:
>
>
>
> 1)  How accurate is the mapping using mri_surf2surf? That is, is it good
> for preliminary data, but not for the final analysis?
>
> 2)  How do you run the cortical parcellation using the Yeo 2011 atlas?
> [I know that mris_ca_train and mris_ca_label exist, but I’m unsure if they
> are the right commands to run when I’m not building my own atlas]
>
> 3)  If I do the cortical parcellations using the Yeo 2011 atlas, will
> the edits/labels I’ve done using the Desikan atlas remain accurate? This
> goes back to the second question, as I’m not sure where in the general
> processing stage I need to go.
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
>
>
> Emma Bailin
>
>
>
> Emma Bailin
>
> Research Coordinator
>
> Laboratory for Visual Neuroplasticity
>
> Schepens Eye Research Institute
>
> Mass. Eye and Ear Infirmary
>
> Harvard Medical School
>
>
>
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Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Corinna,

You can download here:
https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0

Regards,
Thomas


On Thu, Jun 29, 2017 at 5:45 AM, Corinna Bauer  wrote:

> Dear Dr. Yeo,
>
> Our research group is currently trying to segment the Yeo atlas into
> separate labels, but just came across this thread which indicates that you
> have already done this. Would you be willing to re-share the link to your
> previously extracted individual labels from your 7 and 17 networks?
>
> Thank you!
>
> Corinna
>
> On Thu, May 14, 2015 at 4:54 AM, Thomas Yeo  wrote:
>
>> Hi Annie,
>>
>> I have previously extracted individual regions from the 7 and 17
>> networks. You can download them here
>> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol
>> 11_SplitLabels.zip?dl=0).
>> Please see the README in the folder for more explanations. There
>> should be a precuneus DMN region.
>>
>> The 17 networks consist of 114 regions that have been previously
>> published:
>>
>> 1) Krienen et al., Reconfigurable state-dependent functional coupling
>> modes cluster around a core functional architecture. Philosophical
>> Transactions of the Royal Society B, 369:20130526, 2014
>>
>> 2) Yeo et al., Functional connectivity during rested wakefulness
>> predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
>> 2015
>>
>> Hope this helps.
>>
>> Cheers,
>> Thomas
>>
>> On Thu, May 14, 2015 at 3:08 PM, 陳昱潔  wrote:
>> > Hello Dr. Yeo,
>> >
>> > Thank you for your previous help and reply. We've worked out the way to
>> > switch the resolution of parcellation and successfully extracted the
>> > anatomical information using your mask derived from iFC work.
>> >
>> > However, we came across a new problem to apply the cortical mask and
>> need
>> > your kind help again. We aim to conduct a seed-based analysis to
>> investigate
>> > structural covariance based on the network defined by iFC, and find your
>> > work of cortical parcellation conceptually perfectly suit our research
>> > question. Based on the current approach, however, it seemed that we
>> could
>> > only extract the anatomical information from the whole well-defined
>> network,
>> > but not the specific hub within the network (e.g., the anatomical
>> > information of the precuneus from the DMN). We wonder if you have any
>> > suggestion to resolve our problem, ie, to be specific, is there any way
>> to
>> > only extract the discrete hub information rather than the whole network?
>> >
>> > We really appreciate your generous help. Thank you very much.
>> >
>> > p.s. This email would also forward to my senior colleague, Dr.
>> Hsiang-Yuan
>> > Lin, who is a child and adolescent psychiatrist doing imaging research
>> in
>> > Taiwan.
>> >
>> >
>> > 2015-05-13 19:15 GMT+08:00 陳昱潔 :
>> >>
>> >> Hi Professor Yeo :
>> >>
>> >> Thank you for helping us so much!
>> >> After mris_anatomical_stat I tried aparcstats2table to extract the
>> table.
>> >> But I failed with generating the table.
>> >>
>> >>
>> >> Best wishes,
>> >> Annie
>> >>
>> >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo :
>> >>
>> >>> Hi Annie,
>> >>>
>> >>> I assume this means 5202 is your subject ID? Maybe you should check if
>> >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network
>> s_N1000.annot
>> >>> exist?
>> >>>
>> >>> If so, you can run mris_anatomical_stats to generate statistics for
>> >>> the parcellation.
>> >>>
>> >>> Cheers,
>> >>> Thomas
>> >>>
>> >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔  wrote:
>> >>> > Hi Professor Yeo :
>> >>> > After I rechecked the directory and run again mri_surf2surf
>> >>> > I got the result:
>> >>> > "Saving target data
>> >>> > Converting to target annot
>> >>> > Saving to target annot
>> >>> >
>> >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network
>> s_N1000.annot"
>> >>> > The file of 5202/label didn't come out with
>> >>> > lh.Yeo2011_7Networks_N1000.annot
>> >>> > Bu

[Freesurfer] Open Letter to NIH Director Francis Collins

[Thomas Yeo]

Dear Everyone,

Please note the following NIH petition regarding the impending
classification of basic science research as clinical trials:
https://ipetitions.com/petition/open-letter-nih-collins

Regards,
Thomas
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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

[Thomas Yeo]

Hi Chintan,

Sorry. At that time, we wanted to not bias the interpretation of the
networks by naming them. But that may be a bit idealistic. We have
subsequently named the networks.

To map networks 1 to 17 to the names, the easiest way is to load the annot
in freeview and hover your mouse over it and then visually match it to
Figure 1 of this paper (http://people.csail.mit.edu/ythomas/publications/
2015SleepDeprivation-NeuroImage.pdf). When I do so, I get the following,
but you probably want to double check!

1) Network 1: Visual A

2) Network 2: Visual B

3) Network 3: SomMot A

4) Network 4: SomMot B

5) Network 5: DorsAttn A

6) Network 6: DorsAttn B

7) Network 7: Sal/VentAttn A

8) Network 8: Sal/VentAttn B

9) Network 9: Limbic B

10) Network 10: Limbic A

11) Network 11: Control C

12) Network 12: Control A

13) Network 13: Control B

14) Network 14: TempPar

15) Network 15: Default C

16) Network 16: Default A

17) Network 17: Default B

Regards,
Thomas


On Thu, Oct 5, 2017 at 2:54 AM, Mehta, Chintan 
wrote:

> Dear Freesurfer users,
>
> I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The
> regions are labeled 1 through 17. Is there a reference table mapping these
> numbers with the names of cognitive networks described by Yeo, et al.
> (2011) ( 
> https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would network
> 1 correspond to visual networks? I cannot find descriptions in the readme
> files except the color look-up table.
>
>
> Thank you.
>
> Best,
>
> Chintan
>
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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

[Thomas Yeo]

Hi Adam,

Language activations definitely hit Default B, but Default B is also
activated by tasks such as theory of mind (see Figure 4 here:
https://www.biorxiv.org/content/biorxiv/early/2017/06/19/149567.full.pdf),
so I am not sure we can consider it to be a pure language network.

Although there has been papers trying to delineate language networks using
resting-state fMRI, my experience is that it's not something that easily
pops out of resting-state data, compared with task or meta-analytic data
(e.g., see component 5 here:
http://people.csail.mit.edu/ythomas/publications/2015BrainmapInteractive/index.html
)

Regards,
Thomas

On Thu, Oct 5, 2017 at 3:30 PM, Adam Martersteck  wrote:

> Hi Dr. Yeo,
>
> Just a related question -- do you have an opinion on if one of the network
> solutions corresponds to the language network? I realize they are all
> bilateral, with no significantly left lateralized one. But do you think one
> of the DMN solutions (such as Default B in the paper you linked, much more
> representative on the LH surface view) might represent the language network?
>
> -Adam
>
> On Thu, Oct 5, 2017 at 2:07 AM, Thomas Yeo  wrote:
>
>> Hi Chintan,
>>
>> Sorry. At that time, we wanted to not bias the interpretation of the
>> networks by naming them. But that may be a bit idealistic. We have
>> subsequently named the networks.
>>
>> To map networks 1 to 17 to the names, the easiest way is to load the
>> annot in freeview and hover your mouse over it and then visually match it
>> to Figure 1 of this paper (http://people.csail.mit.edu/y
>> thomas/publications/2015SleepDeprivation-NeuroImage.pdf). When I do so,
>> I get the following, but you probably want to double check!
>>
>> 1) Network 1: Visual A
>>
>> 2) Network 2: Visual B
>>
>> 3) Network 3: SomMot A
>>
>> 4) Network 4: SomMot B
>>
>> 5) Network 5: DorsAttn A
>>
>> 6) Network 6: DorsAttn B
>>
>> 7) Network 7: Sal/VentAttn A
>>
>> 8) Network 8: Sal/VentAttn B
>>
>> 9) Network 9: Limbic B
>>
>> 10) Network 10: Limbic A
>>
>> 11) Network 11: Control C
>>
>> 12) Network 12: Control A
>>
>> 13) Network 13: Control B
>>
>> 14) Network 14: TempPar
>>
>> 15) Network 15: Default C
>>
>> 16) Network 16: Default A
>>
>> 17) Network 17: Default B
>>
>> Regards,
>> Thomas
>>
>>
>> On Thu, Oct 5, 2017 at 2:54 AM, Mehta, Chintan 
>> wrote:
>>
>>> Dear Freesurfer users,
>>>
>>> I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The
>>> regions are labeled 1 through 17. Is there a reference table mapping these
>>> numbers with the names of cognitive networks described by Yeo, et al.
>>> (2011) ( <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/>
>>> https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would
>>> network 1 correspond to visual networks? I cannot find descriptions in the
>>> readme files except the color look-up table.
>>>
>>>
>>> Thank you.
>>>
>>> Best,
>>>
>>> Chintan
>>>
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>>>
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>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
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>>> HelpLine at
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>>> in error
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>>> properly
>>> dispose of the e-mail.
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>>>
>>
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>>
>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose 

[Freesurfer] New Openings for Postdoctoral Fellows

[Thomas Yeo]

Dear Everyone,

My lab has new openings for postdoctoral fellows. Please see job
descriptions here: https://yeolab.weebly.com/jobs.html

Thanks,
Thomas
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Re: [Freesurfer] Yeo atlas FreeSurfer

[Thomas Yeo]

Hi Martin,

We have previously split the networks into 114 regions:
https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeurophysiol11_SplitLabels.
zip?dl=0 . See Figure 1 in the first reference below. If you decide to use
these regions, please kindly cite the following papers:

1) Yeo BTT, Tandi J, Chee MWL. Functional connectivity during rested
wakefulness predicts vulnerability to sleep deprivation. Neuroimage
111:147-158, 2015

2) Krienen FM, Yeo BTT, Buckner RL. Reconfigurable state-dependent
functional coupling modes cluster around a core functional architecture.
Philosophical Transactions of the Royal Society B, 369:20130526, 2014

Thanks,
Thomas

On Wed, Oct 18, 2017 at 3:48 AM, Martin Juneja  wrote:

> Hi experts,
>
> I am using Yeo atlas (7 networks) in my analysis. Where can I find name of
> all the regions involved in each of these 7 networks in Yeo atlas?
>
> Thanks.
>
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Re: [Freesurfer] Yeo atlas FreeSurfer

[Thomas Yeo]

Hi Martin,

Those postfix are based on anatomical location. If you load the parcels on
freeview with the associated colortable, you should be able to infer what
the postfix are referring to.

Off the top of my head (but you should double check by loading on freeview):

1) FrOper = frontal operculum

2) PFCl = Prefrontal Cortex Lateral

3) FEF = frontal eye fields

4) ParOper = parietal operculum

5) TempOcc = temporal occipital

6) PHC = parahippocampal complex

7) PFCmp = I think mp stands for medial posterior, but I am not super sure,
you probably want to visualize this and double check.

Thanks,
Thomas

On Thu, Oct 19, 2017 at 1:16 AM, Martin Juneja  wrote:

> Dear Dr. Yeo,
>
> Thanks a lot for your reply.
> Actually, I have already analyzed the effect of treatment on these 7
> functional networks. I just want to report what are the areas which
> constitute each of these network.
>
> Somehow in the reference you sent, I could not find name of each regions
> of interest which are part of these networks. In the zip folder you sent, I
> found following information. Is there a way I can still get full name of
> ROIs e.g. here I do not know FrOper, PFCI etc.
>
> I would really appreciate any help.
>
> Thanks !
>
> *Network 1:*
> 1 7Networks_LH_Vis 120  18 134   0
>
> *Network 2:*
>   2  7Networks_LH_SomMot  70 130 180   0
>
> *Network 3:*
>   3   7Networks_LH_DorsAttn_Post   0 118  14   0
>   47Networks_LH_DorsAttn_FEF   0 118  15   0
>   5   7Networks_LH_DorsAttn_PrCv   0 119  14   0
>
> *Network 4:*
>   6 7Networks_LH_SalVentAttn_ParOper 196  58 250   0
>   7 7Networks_LH_SalVentAttn_TempOcc 196  58 251   0
>   8  7Networks_LH_SalVentAttn_FrOper 196  59 250   0
>   97Networks_LH_SalVentAttn_PFCl 196  59 251   0
>  10 7Networks_LH_SalVentAttn_Med 197  58 250   0
>
> *Network 5:*
>  11  7Networks_LH_Limbic_OFC 220 248 164   0
>  12 7Networks_LH_Limbic_TempPole 220 248 165   0
>
> *Network 6:*
>  137Networks_LH_Cont_Par 230 148  34   0
>  14   7Networks_LH_Cont_Temp 230 148  35   0
>  15   7Networks_LH_Cont_PFCd 230 149  34   0
>  16   7Networks_LH_Cont_PFCl 230 149  35   0
>  177Networks_LH_Cont_OFC 231 148  34   0
>  18   7Networks_LH_Cont_PFCv 231 148  35   0
>  19   7Networks_LH_Cont_pCun 231 149  34   0
>  20   7Networks_LH_Cont_Cing 231 149  35   0
>  21  7Networks_LH_Cont_PFCmp 230 148  33   0
>
> *Network 7:*
>  22 7Networks_LH_Default_Par 205  62  78   0
>  237Networks_LH_Default_Temp 205  62  79   0
>  24 7Networks_LH_Default_PFC 205  63  78   0
>  25     7Networks_LH_Default_PCC 205  63  79   0
>  26 7Networks_LH_Default_PHC 206  62  78   0
>
>
> On Wed, Oct 18, 2017 at 6:44 AM, Thomas Yeo  wrote:
>
>> Hi Martin,
>>
>> We have previously split the networks into 114 regions:
>> https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeur
>> ophysiol11_SplitLabels.zip?dl=0 . See Figure 1 in the first reference
>> below. If you decide to use these regions, please kindly cite the
>> following papers:
>>
>> 1) Yeo BTT, Tandi J, Chee MWL. Functional connectivity during rested
>> wakefulness predicts vulnerability to sleep deprivation. Neuroimage
>> 111:147-158, 2015
>>
>> 2) Krienen FM, Yeo BTT, Buckner RL. Reconfigurable state-dependent
>> functional coupling modes cluster around a core functional architecture.
>> Philosophical Transactions of the Royal Society B, 369:20130526, 2014
>>
>> Thanks,
>> Thomas
>>
>> On Wed, Oct 18, 2017 at 3:48 AM, Martin Juneja  wrote:
>>
>>> Hi experts,
>>>
>>> I am using Yeo atlas (7 networks) in my analysis. Where can I find name
>>> of all the regions involved in each of these 7 networks in Yeo atlas?
>>>
>>> Thanks.
>>>
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Re: [Freesurfer] Region in Yeo_17Network_16 as seed in FS-FAST

[Thomas Yeo]

Hi Stefano,

The Yeo 17 networks have been extracted into 114 regions in fsaverage space
(
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
).

You can map them to individual subjects' space using mri_surf2surf.

Regards,
Thomas

On Sat, Mar 3, 2018 at 7:48 PM,  wrote:

> Hi list,
>
> I should use the the region describing the mPFC in Yeo_17Network_16 (DMN)
> as a seed in FS-FAST (FC analysis)
>
> How can I do to isolated this regions?
>
> Thanks
>
>
> Stefano
>
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Re: [Freesurfer] Fw: Yeo Atlas Network 3 segmentation FEF

[Thomas Yeo]

External Email - Use Caution

Hi Catherine,

We have extracted the 7 and 17 networks into 51 and 114 regions
respectively. See figures in
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering

Unfortunately, we have only provided the parcellation in fsaverage5 (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels),
so you should add one more mri_surf2surf step to upsample the parcellation
from fsaverage5 to fsaverage. Check that it is good and then proceed with
your previous steps.

I am emailing the freesurfer list, so that my reply might hopefully be
useful for other folks.

Regards,
Thomas

On Thu, May 3, 2018 at 8:46 AM, Catherine Joe 
wrote:

> Hello Dr Yeo,
>
>
> Yes, I want to be able to split network 3 into different component regions
> so that I can have a nii file for FEF. This will then allow me to get the
> signal intensity and hopefully, the volume of the FEF region for each
> participant in my Honour's project.
>
>
> Thank you.
>
>
> Kind regards,
>
> Catherine
> --
> *From:* Thomas Yeo 
> *Sent:* Thursday, 3 May 2018 9:36:52 AM
>
> *To:* Catherine Joe
> *Cc:* 李婧玮
> *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
>
> Hi Catherine,
>
> Can I verify what you need is network 3 split into different component
> regions like FEF, etc?
>
> Regards,
> Thomas
>
> On Wed, May 2, 2018 at 11:08 AM Catherine Joe 
> wrote:
>
> Hi Dr Yeo and Jingwei,
>
>
> Yes, I did use that link to subscribe to the mailing list about 2.5 weeks
> ago and they still haven't gotten back to me. I simply thought I didn't get
> a confirmation email and tried again, which was the message I forwarded to
> you today. Just now, I tried subscribing again.
>
>
> So the commands I've used so far is as follows:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject subject11GS --hemi lh
> --sval-annot $subjectdir/Yeo_Neurophysiol11_Freesurfer/
> fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval lh.7Networks.annot
>
> (same was done for the rh before doing mri_aparc2aseg)
>
>
> mri_aparc2aseg --s subject11GS --o $subjectdir/subject11GS/test/test.mgz
> --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorlux.txt
>
>
> mri_annotation2label --subject subject11GS --outdir
> $subjectdir/subject11GS/test --hemi lh --annotation
> $subjectdir/subject11GS/label/lh.7Networks.annot
>
>
> mri_label2vol --label $subjectdir/subjet11GS/test/lh.7Networks_3.label
> --temp $subjectdir/subject11GS/mri/rawavg.mgz --subject subject11GS
> --hemi lh 00o $subjectdir/subject11GS/test/lh7Networks.nii.gz --proj frac
> 0 1 0.01 --reg $subjectdir/subject11GS/corticalroi/subject11GS_
> register.dat
>
>
> And after doing that, all I got was the volume for network 3 but not
> actually having any separation with the FEF and the other areas.
>
>
> Thank you for your help.
>
>
> Kind regards,
>
> Catherine
>
> --
> *From:* yeoye...@gmail.com  on behalf of Thomas Yeo <
> ytho...@csail.mit.edu>
> *Sent:* Wednesday, 2 May 2018 10:33:18 AM
> *To:* Catherine Joe
> *Cc:* 李婧玮
> *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
>
> Hi Catherine,
>
> Have you tried subscribing to the mailing here (
> http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)?
>
> Can you please let me know the exact commands you have tried so far?
>
> I am cc-ing my grad student (Jingwei), who might be able to answer more
> rapidly. Please reply all to keep her in the loop.
>
> Thanks,
> Thomas
>
> On Wed, May 2, 2018 at 8:14 AM, Catherine Joe 
> wrote:
>
> Hi Dr Yeo,
>
>
> Thank you for your help before with actually aligning and extracting your
> atlas. I know that you mentioned before that I should try and email into
> the FreeSurfer mailing list for any further queries.
>
> However, as you can see, I am apparently not subscribed to the list even
> though I sent in a request before. I've been trying to send in a question
> for the past week.
>
> I was wondering if you'd be able to help me with this problem I've had
> after extracting the Network 3 ROI. The message I tried sending to the
> FreeSurfer Mailing list is as below:
>
>
> Hello,
>
>
> I'm having trouble getting the segmentation for the FEF using the Yeo
> Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume
> file, it doesn't show me two individual labels for the network (primarily
> the three areas of the dorsal attent

Re: [Freesurfer] Projecting meta-analytic map on the surface

[Thomas Yeo]

External Email - Use Caution

Hi Srishti,

We recently wrote a paper on projecting data from Colin27/MNI152 to
fsaverage surface (https://www.biorxiv.org/content/early/2018/04/27/302794).
The paper is in press at HBM.

The code is available here:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Thu, May 10, 2018 at 9:03 AM, srishti goel <23srishtig...@gmail.com>
wrote:

> External Email - Use Caution
>
> Hello Freesurfers,
>
> I have a network based map that has been produced from a meta analysis
> using NeuroElf on the standard colins template. I want to project this map
> on the surface of an MNI template.
> Does anyone have thoughts about how that could be achieved?
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
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Re: [Freesurfer] Yeo-2011 individual ROIs

[Thomas Yeo]

External Email - Use Caution

Hi Ehsan,

Not sure if any is exactly what you need:

1) We have divided the 7 and 17 networks into 51/114 ROIs (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
Note that these are group-level parcellations in fsaverage space, so you
have to use mri_surf2surf to project to individual subjects' surface.

2) We have also released code for 17-network parcellation of individual
subjects' resting-fMRI data (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Kong2019_MSHBM
).

3) Finally, we have released a 400-region parcellation, as well as other
resolutions (100 to 1000 parcels), which map to the original 7 and 17
networks (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
).

Regards,
Thomas

On Thu, Jul 19, 2018 at 12:51 AM Ehsan Tadayon 
wrote:

> External Email - Use Caution
>
> Hi,
>
> Is there an easy way to sub-parcellate each network in Yeo-2011 (for
> instance network 7) into several clusters (ROIs) for an individual subject?
>
> thanks
> Ehsan.
>
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Re: [Freesurfer] R: Re: Yeo parcellation

[Thomas Yeo]

Hi Stefano,

Here's what you can do. In your shell (assuming you are using c shell)

# First set variable s to be subject id
>> set s = 100306_QD95CU_FS

# set freesurfer environmental variable SUBJECTS_DIR to point to where
the data is
>> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/

# use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage

# use "-sval-annot" option to transfer annotation
>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot 
>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot

# use "sval" option to transfer confidence map.
>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>>  --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz

Cheers,
Thomas


On Sun, Jul 20, 2014 at 10:33 PM,   wrote:
> Hi list and Thomas,
>
> I'm running the first step to use Yeo's parcellation. The running is wrong.
>
> mri_surf2surf --s Control01 --hemi lh --sval-tal-xyz white --tval
> lh.white.Control01 --tval-xyz --trgsubject
> fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz
>
> Reading target surface reg
> $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg
> MRISread(
> $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg):
> could not open file
> Not a directory
> mri_surf2surf: could not read surface
> $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg
>
> Thanks,
>
>
> Stefano
>
>
> Messaggio originale
> Da: ytho...@csail.mit.edu
> Data: 7-feb-2014 9.49
> A: 
> Cc: "freesurfer"
> Ogg: Re: [Freesurfer] Yeo parcellation
>
> Hi Stefano,
>
> A) From FreeSurfer 5.2 onwards, the Yeo parcellation files can be
> found inside $FREESURFER_HOME/subjects/fsaverage/label/, so you can
> simply use those files there instead of downloading from the wiki.
>
> B) You can use mri_surf2surf to transform the annot files from the
> fsaverage "subject" to the individual subjects' surface. There is an
> example of how to do it if you run "mri_surf2surf --help"
>
> C) Once you have created the subject's specific annot file from part
> B, I believe you must first run mris_anatomical_stats, and then run
> aparcstats2table. However, I am not sure about this, so someone on the
> list should correct me if I am wrong!
>
> Regards,
> Thomas
>
> On Fri, Feb 7, 2014 at 3:58 PM,   wrote:
>> Hi list,
>>
>> I have download the files of Yeo parcellation from
>> ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip.
>>
>> I have two questions, please.
>>
>> A- Which is the directory where I should put these files?
>> B-I have already run by recon-all -all all my subjects. How can I added to
>> them Yeo parcellation?
>> C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is
>> possible with aparcstats2table?
>>
>> Thanks.
>>
>> Regards,
>>
>>
>> Stefano
>>
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Re: [Freesurfer] Which Freesurfer regions in Default mode network ?

[Thomas Yeo]

Hi Mehul,

You can use the resting-state fMRI-defined default network
regions in fsaverage space. See
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011.
Note that the parcellation is now part of FreeSurfer official release.
See relevant publication in wiki.

Cheers,
Thomas

On Tue, Aug 26, 2014 at 12:07 PM, Mehul Sampat  wrote:
> Hi Folks,
>
> I wanted to ask which Freesurfer regions from aparc+aseg.mgz are included in
> Default mode network ? Is there a relevant publication on this topic ?
> Thanks
> Mehul
>
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[Freesurfer] Brainmap Ontology

[Thomas Yeo]

Dear FreeSurfer List,

I like to introduce you to a new set of reference brain networks
(cognitive components) estimated from 10,449 experiments and 83
behavioral tasks from the BrainMap database, which can be downloaded
here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015.
The networks will be incorporated in some future version of
FreeSurfer.

Since these networks are estimated from (meta-analytic) task data,
they are meant to complement (not replace) the current resting-state
networks in FreeSurfer
(https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)

Cheers,
Thomas
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[Freesurfer] Postdoctoral Fellow in Analysis of Cross-Species fMRI and/or Neurophysiology

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop novel tools for fMRI and/or
neurophysiology analysis. Details below.

Cheers,
Thomas

Project: Develop computational tools for discovering (1) homologies
and divergences between macaque and human brain organization using
resting-fMRI and/or (2) relationship between macaque brain network
organization revealed by fMRI versus neurophysiological recordings.

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Postdoctoral Fellow in Human-Macaque Brain Network Organization

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc in human-macaque brain organization.
Details below.

Cheers,
Thomas

Project: (1) Discover homologies and divergences between macaque and
human brain organization using resting-fMRI and/or (2) Elucidate
relationship between macaque brain network organization revealed by
fMRI versus neurophysiological recordings.

Requirements: PhD in neuroscience, psychology, cognitive science or
related fields. The successful applicant will work with an
interdisciplinary team of computer scientists and neuroscientists, and
must be willing to do some programming.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: The National University of Singapore (NUS) boasts one of
the few primate neurophysiology labs in the world. Perform
ground-breaking research at NUS, while enjoying the beautiful
sceneries and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Resample the surface mesh

[Thomas Yeo]

Hi Ting,

I am not an expert, but why do you want to downsample the native
surface mesh? The usual way of doing this is to register the full
surface mesh with the functional volume data using Doug's bbregister.

Cheers,
Thomas

On Fri, Nov 21, 2014 at 4:08 AM, ting xu  wrote:
> Dear freesurfer experts,
>
> Is there any way to down resample the native surface mesh and register the
> functional volume data to the down resampled surface in freesurfer?
>
> Many thanks,
>
> Ting
>
>
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Re: [Freesurfer] Resample the surface mesh

[Thomas Yeo]

Hi Ting,

What I usually do is to project my functional data to fsaverage space
and then smooth and downsample to whatever resolution I want. There
are different fsaverage resolution meshes, like fsaverage5 (~20k
vertices) and fsaverage6 (~80k vertices). This can be achieved using
standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note
that in this scenario, even though the data is in fsaverage space,
this does not preclude individual subject analysis. The advantage of
the above approach is that we can still easily perform a group
analysis if we want to in the future.

The disadvantage is that we lose a little bit of the subject's native
cortical geometry, which is not an issue for your proposed approach.
However, I am not aware of freesurfer tools that will let you
downsample an arbitrary mesh. Perhaps someone who is more intimately
aware of freesurfer's tools can jump in on this.

Cheers,
Thomas

On Mon, Nov 24, 2014 at 5:10 AM, ting xu  wrote:
> Hi Thomas,
>
> I want to analyze the data in native surface space. The functional volume
> data could be register to native surface with bbregister, however, the
> resolution of the native surface is quite high, too much nodes for
> computational capacity to me. Any ideas?
>
> Thanks,
>
> Ting
>
>
> On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo  wrote:
>>
>> Hi Ting,
>>
>> I am not an expert, but why do you want to downsample the native
>> surface mesh? The usual way of doing this is to register the full
>> surface mesh with the functional volume data using Doug's bbregister.
>>
>> Cheers,
>> Thomas
>>
>> On Fri, Nov 21, 2014 at 4:08 AM, ting xu  wrote:
>> > Dear freesurfer experts,
>> >
>> > Is there any way to down resample the native surface mesh and register
>> > the
>> > functional volume data to the down resampled surface in freesurfer?
>> >
>> > Many thanks,
>> >
>> > Ting
>> >
>> >
>> > ___
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>> >
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Re: [Freesurfer] resampling method to transform EPI vol to surf

[Thomas Yeo]

Hi Ri,

The command you provide just register (align) the EPI data with the T1
image. It doesn't actually tell us how you sample your data onto the
surface. Presumably you must have used mri_vol2surf (at least
implicitly) to use the resultant registration to sample your data onto
the surface. What is the exact command you use?

Cheers,
Thomas


On Tue, Dec 23, 2014 at 7:26 PM, Ritobrato Datta
 wrote:
> Hi All,
>
> For a reviewer, I need the following ASAP:
>
> Comments from Reviewer: Please provide a brief description of the resampling 
> method by which volume data were transformed to surface data. Was the data 
> averaged between the white and pial boundaries? Or was a constant normal 
> average taken?
>
> I used bbregister as follows to register the epi image to freesurfer anatomy
>
> bbregister --s $Subject --bold --mov Functional-FS.nii --init-fsl --reg 
> FS-register.dat
>
> Can someone comment on the resampling method as the reviewer asked ?
>
> Thanks
>
> Ri
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Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

[Thomas Yeo]

External Email - Use Caution

Hi Katherine,

Yes. This is still the best way if you have already run recon-all.

Regards,
Thomas

On Sat, Oct 6, 2018 at 8:21 AM Katherine Damme 
wrote:

> Hello,
>
> I have a tone of FS people who have been run through Recon-all and I am
> happy with the output but I would like to expand the existing labels to
> include the Buckner 7 tight labels. Is this still the best way to update my
> subject labels to include these labels?
>
> On Sat, Nov 26, 2016 at 8:07 PM Thomas Yeo  wrote:
>
>> Hi Noam,
>>
>> This should be a two step procedure, rather than a one-step procedure.
>> Here's a previous email I sent to the list about warping Choi's
>> striatum atlas to individual subject's striatum (which I have modified
>> for the cerebellum for you). Let us know if this works.
>>
>> 1) Assuming you are quite happy with the freesurfer cerebellum
>> parcellation in your subjects, then I am assuming freesurfer nonlinear
>> registration (talairach.m3z) is working quite well. Talairach.m3z
>> warps your subject to an internal freesurfer space (kinda like MNI305,
>> but not quite). Let's say the freesurfer recon-all output is at
>> /SUBJECT_FS/
>>
>> 2) Run the MNI152 1mm template (the one from FSL) through recon-all.
>> Recon-all will give you a Talairach.m3z that allows you to map the
>> MNI152 1mm template to the internal freesurfer space. Let's say the
>> freesurfer recon-all output is at /MNI152_FS/
>>
>> 3) Then do the following:
>>
>> a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
>> 2mm resolution to the 1mm MNI152 template:
>>
>> >> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
>> --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
>>
>> Notice that I use norm.mgz of the MNI template rather than the
>> original MNI template. norm.mgz is the 256 x 256 x 256 conformed
>> version of the MNI template that recon-all puts through.
>>
>> b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric
>> space:
>>
>> >> setenv SUBJECTS_DIR 
>> >> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>> Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
>>
>> c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your
>> subject:
>>
>> >> setenv SUBJECTS_DIR 
>> >> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
>> --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z
>> --o Buckner_atlas_subject.nii.gz --interp nearest --inv-morph
>>
>> This is not optimal because of the double interpolation. You might
>> want to use the MNI template instead of the Buckner_atlas to test the
>> above, so you can check the goodness of the warp. The final warped MNI
>> template should hopefully look identical to your subject. If that
>> works, then use the Buckner_atlas. Note that mri_vol2vol does not work
>> properly for talairach.m3z below version 5, so you should use version
>> 5x mri_vol2vol.
>>
>> Regards,
>> Thomas
>>
>> On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam 
>> wrote:
>> > Dear group,
>> > I'm trying to morph the Buckner2011 cerebellum segmentation map from
>> MNI152
>> > to subject's space:
>> > mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ
>> > Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> --m3z
>> > talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest
>> > --inv-morph
>> > It worked with the 17 networks, but didn't work with the 7 networks
>> version.
>> > Any ideas? This is really strange.
>> >
>> > Thanks,
>> > Noam
>> > (function(){(function n(e) { "use strict"; function t(e) { if
>> (e.parentNode)
>> > if (e.childNodes.length > 1) { for (var t =
>> > document.createDocumentFragment(); e.childNodes.length > 0; ) { var n =
>> > e.childNodes[0]; t.appendChild(n); } e.parentNode.replaceChild(t, e); }
>> else
>> > e.firstChild ? e.parentNode.replaceChild(e.firstChild, e) :
>> > e.parentNode.removeChild(e); } function n(e) { if (e) try { for (var n =
>> > e.querySelectorAll(".gr_"), r = n.length, o = 0; r > o; o++) t(n[o]); }
>> > catch (i) {} } function r(e) { try { Object.defineProperty(e,
>>

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

External Email - Use Caution

Hi Bronwyn,

I know it's been a long time, but my RA recently explored this and we think
that mri_aparc2aseg might be a better option that mri_label2vol. Anyway,
here's the updated process for mapping the Yeo2011 networks from fsaverage5
to individual volumetric space:

1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) *Transform from subject's surface into your subject's volume*
Instead of using "mri_label2vol", we now recommend using "mri_aparc2aseg".
This will give you ROIs that fully cover subject's grey matter.

mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion:
a) Find the indices of left/right cerebral cortex by extracting the voxels
with a value of 3 or 42 in the subject's aseg.
b) Use those indices to mask out the voxels that are not cerebral cortex in
your outputfile.mgz file (i.e. set non cerebral cortical voxels to be 0).
c) For the cortical voxels, you may subtract 1000 for those between 1000
and 2000; and subtract 2000 for those greater than 2000.

Thanks,
Thomas

On Thu, Jun 23, 2016 at 2:26 PM Bronwyn Overs  wrote:

> Thanks very much Thomas.
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
> <https://www.facebook.com/NeuroscienceResearchAustralia>[image: Subscribe
> to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe>
> On 23/06/2016 4:20 pm, Thomas Yeo wrote:
>
> You should be able to use the 5.3 version.
>
> Regards,
> Thomas
>
> On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs 
> wrote:
>
>> Hi Thomas,
>>
>> Thanks for your reply.
>>
>> The fsaverage directory I have for fs v 5.1 does not include the lh and
>> rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version
>> of fsaverage. Can I still use the 5.3 version annot files or would I need a
>> seperate set processed with version 5.1?
>>
>> Kind regards,
>>
>> Bronwyn Overs
>> Research Assistant
>> [image: Neuroscience Research Australia]
>>
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> *M* 0411 308 769 *T* +61 2 9399 1883 <%2B61%202%209399%201883>
>> neura.edu.au
>>
>> [image: Follow @neuraustralia on twitter]
>> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook]
>> <https://www.facebook.com/NeuroscienceResearchAustralia>[image:
>> Subscribe to the NeuRA Magazine]
>> <http://www.neura.edu.au/help-research/subscribe>
>> On 23/06/2016 3:17 pm, Thomas Yeo wrote:
>>
>> Hi Bronwyn,
>>
>> You raise a good point. You can consider creating a cortical mask using
>> aparc+aseg.mgz and use that to mask the networks.
>>
>> However, another approach (which might be more accurate) is to take
>> cortical networks in fsaverage space and transform to your subject's
>> surface and then transform into your subject's volume:
>>
>> # Transform from fsaverage to subject's surface
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi
>> lh --sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
>> $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*
>>
>> # Transform from subject's surface into your subject's volume (I am not
>> super sure about this. You probably want to double check the output is
>> correct)
>> >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
>> outfile.nii.gz --hemi lh --subject HS_001 **--regheader*
>>
>> --Thomas
>>
>> On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs 
>> wrote:
>>
>>> Hi Mailing List,
>>>
>>> I am attempting to apply the Ye

Re: [Freesurfer] Cortical Parcellations in individual space using Yeo et al 2011

[Thomas Yeo]

External Email - Use Caution

Hi Emma,

I know it's been a long time, but my RA recently explored this and we think
that mri_aparc2aseg might be a better option that mri_label2vol. Anyway,
here's the updated process for mapping the Yeo2011 networks from fsaverage5
to individual volumetric space:

1) Transform from fsaverage to subject's surface
mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) Transform from subject's surface into your subject's volume
Instead of using "mri_label2vol", we now recommend using "mri_aparc2aseg".
This will give you ROIs that fully cover subject's grey matter.

mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion:
a) Find the indices of left/right cerebral cortex by extracting the voxels
with a value of 3 or 42 in the subject's aseg.
b) Use those indices to mask out the voxels that are not cerebral cortex in
your outputfile.mgz file (i.e. set non cerebral cortical voxels to be 0).
c) For the cortical voxels, you may subtract 1000 for those between 1000
and 2000; and subtract 2000 for those greater than 2000.

Thanks,
Thomas

On Wed, Feb 15, 2017 at 11:52 AM Thomas Yeo  wrote:

> Hi Emma,
>
> I recommend that you follow the mri_surf2surf and mri_label2vol route.
> As recommended in the other emails, you should probably load the
> resulting parcellations and make sure they look ok.
>
> As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so
> applicable here because they require multiple subjects with
> resting-state parcellations in order to train the classifier. We are
> working on an individual subject 7-network and 17-network parcellation
> algorithm, but it's not ready yet.
>
> What kind of edits have you already done? If your edits involve
> correcting the gray/white matter segmentation and the cortical
> surfaces, then your edits should be reflected (since mri_surf2surf and
> mri_label2vol should utilized the updated cortical surfaces). However,
> if your edits involving editing the Desikan's parcellation itself,
> then probably not.
>
> Regards,
> Thomas
>
> On Wed, Feb 15, 2017 at 6:11 AM, Bailin, Emma
>  wrote:
> > Hello,
> >
> >
> >
> > I’m preparing to do resting state analyses and I’d like to use the Yeo
> 2011
> > network atlas for the cortical parcellations. Looking through the
> archive, I
> > know that mri_surf2surf with the –sval-annot flag can be used to convert
> the
> > fsaverage from the Yeo et al 2011 study to an individual subject space,
> but
> > I noticed a caveat to this when I called mri_surf2surf –help. The caveat
> is
> > on example 5: “this is not a substitute for running the cortical
> > parcellation! The parcellations that it maps to the new subject may not
> be
> > appropriate for that subject.”
> >
> >
> >
> > Given this information, I’ve got a few questions:
> >
> >
> >
> > 1)  How accurate is the mapping using mri_surf2surf? That is, is it
> good
> > for preliminary data, but not for the final analysis?
> >
> > 2)  How do you run the cortical parcellation using the Yeo 2011
> atlas?
> > [I know that mris_ca_train and mris_ca_label exist, but I’m unsure if
> they
> > are the right commands to run when I’m not building my own atlas]
> >
> > 3)  If I do the cortical parcellations using the Yeo 2011 atlas, will
> > the edits/labels I’ve done using the Desikan atlas remain accurate? This
> > goes back to the second question, as I’m not sure where in the general
> > processing stage I need to go.
> >
> >
> >
> > Thank you!
> >
> >
> >
> > Sincerely,
> >
> >
> >
> > Emma Bailin
> >
> >
> >
> > Emma Bailin
> >
> > Research Coordinator
> >
> > Laboratory for Visual Neuroplasticity
> >
> > Schepens Eye Research Institute
> >
> > Mass. Eye and Ear Infirmary
> >
> > Harvard Medical School
> >
> >
> >
> > Mass. Eye and Ear Confidentiality Notice: This e-mail and any files
> > transmitted with it are confidential and are intended solely for the use
> of
> > the indi

Re: [Freesurfer] Cerelellar parcellation labels Request

[Thomas Yeo]

External Email - Use Caution

Hi Fan,

Yes. It seems that the link to the SUIT atlas is outdated. However, we are
not the SUIT developers. You should consult the SUIT package (
http://www.diedrichsenlab.org/imaging/suit.htm) :)

Regard,
Thomas

On Thu, Nov 8, 2018 at 1:48 PM dongnandi1  wrote:

> External Email - Use Caution
>
> Hi Freesurfer experts,
>
> The cerebellar 7 and 17 networks parcellation cannot be downloaded.
>
> The link to cerebellar parcellation in SUIT is out of date too.
>
>
>
> so, if you can kindly share the cerebellar 17-network parcellation and
> their anatomy labels, I would be particularly grateful!
>
>  Best wishes
>
>
> Fan
>
> 2018/11/08
>
>
>
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Re: [Freesurfer] Map image in MNI onto fsaverage

[Thomas Yeo]

External Email - Use Caution

Hi John,

Not sure if you still need this, but you can use our approach instead:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Tue, Nov 20, 2018 at 2:15 AM john Anderson 
wrote:

> External Email - Use Caution
>
> Dear Freesurfer experts,
> I have the mean PET images for a number of subjects in MNI152 space. For
> visualization purposes, I would like to map this mean image onto brain
> surface. How can I do it. I appreciate any suggestion you may provide.
> Thanks!
> John
>
>
>
>
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Re: [Freesurfer] Yeo labels

[Thomas Yeo]

External Email - Use Caution

Hi Duygu,

I don't think that's the case at this moment. We usually use the following
command:

mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot

Thanks,
Thomas

On Wed, Jan 9, 2019 at 9:25 AM Tosun, Duygu  wrote:

> External Email - Use Caution
>
> Is there a recon-all flag similar to -label_v1 or -ba-labels to
> automatically create label and stat files for Yeo network parcellations?
>
>
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Re: [Freesurfer] Converting MNI152 coorindates to fsaverage space

[Thomas Yeo]

External Email - Use Caution

Hi Tim,

Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is
different from fsaverage: one is a volumetric space and one is a surface
space.

If you are indeed looking for a transformation between MNI152 volumetric
space and fsaverage surface space, you can consider the following:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer  wrote:

> External Email - Use Caution
>
> > Dear list,
> >
> > I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
> 49.7') in MNI152 space. I would like to transform them to fsaverage space.
> >
> > How should I do that?
> >
>
> To answer my own question, this seems to be explained as use case #8 on
> the following website (at the bottom):
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
> To be precise, the website explains the transformation in the opposite
> direction, so one should use the inverse of the matrix given on the website.
>
> --
> Tim
>
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

You can try the following

1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) *Transform from subject's surface into your subject's volume*
mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz.

Thanks,
Thomas

On Fri, Mar 8, 2019 at 7:29 PM  wrote:

> External Email - Use Caution
>
> Hi Doug,
>
> my apologies, I have tried to do it with some errors. Could you suggest
> the command line, please?
>
> Stefano
>
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
>
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
>
> External Email - Use Caution
>
> Hi list,
>
> I'd like to use the regions included in Yeo 17 networks
> (
> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
> ).
>
> in FS-FAST.
>
> Which is the command line to be used to create a segmentation in
> $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
>
> Thanks
>
> Stefano
>
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but
Yeo_17Net.mgz is empty?

Your tkmedit command seems to assume Yeo_17Net.mgz is in
/Applications/freesurfer/subjects/subject_prova/. But shouldn't the output
be in the mri folder?


On Sat, Mar 9, 2019 at 5:47 PM  wrote:

> External Email - Use Caution
>
> I have run:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
>
> to check the output
>
> tksurfer subj rh inflated -annot
> $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
>
>
> My concern is here:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
>  --sval-annot
> yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
>
>
> tkmeditfv fsaverage orig.mgz -ov
> /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
>
> Yeo_17Net.mgz is empty.
>
>
>
> Stefano
>
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
>
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
>
> External Email - Use Caution
>
> Hi list,
>
> I'd like to use the regions included in Yeo 17 networks
> (
> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
> ).
>
> in FS-FAST.
>
> Which is the command line to be used to create a segmentation in
> $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
>
> Thanks
>
> Stefano
>
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Re: [Freesurfer] Using Schaefer 2018 atlas with FreeSurfer

[Thomas Yeo]

External Email - Use Caution

Hi Fatih,

Instead of mri_label2vol and mri_concat, you can simply call

mri_aparc2aseg --s yoursubject --annot
Schaefer2018_400Parcels_7Networks_order_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion.

We are working on an addition to recon-all, but it won't be so quick :)

Thanks,
Thomas

On Fri, Mar 15, 2019 at 4:26 AM Fatih SOĞUKPINAR <
fatihsogukpina...@gmail.com> wrote:

> External Email - Use Caution
>
>   Dear FreeSurfer developers
>  *For my MRI data, I have cortical parcellations and segmentations for
> the Destrieux and Desikan-Killiany atlases. Now, **I am attempting to use
> Schaefer 2018 atlas
> (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
> )
> for cortical parcellation together with FreeSurfer. Currently what I have
> tried is:*
>
>  *1)* mri_surf2surf --srcsubject fsaverage --trgsubject $SubjectID --hemi
> lh --sval-annot
> /ourSchaferAtlasDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order.annot
> --tval
> ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot
>  *2) *the same of 1) for the right hemisphere
>  *3) *mri_label2vol --annot
> ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot
> --temp  ourSubjectDirectory/mri/our T1.nii --o
> ourSubjectDirectory/mri/sch_lh.mgz --subject $SubjectID --identity --hemi lh
> * 4) * the same of 3) for the right hemisphere
> * 5)* mri_concat ourSubjectDirectory/mri/sch_lh.mgz
> ourSubjectDirectory/mri/sch_rh.mgz --sum --o
> ourSubjectDirectory/mri/sch_lh+rh.mgz
>
> However, at this point, the resulting .mgz file (sch_lh+rh.mgz) is a bit
> strange : When I open the file in matlab, I see that it's volume field is
> 218*182*182 , while the same data results in 256*256*256 for Destrieux
> Atlas. Furthermore, values of the volume field of sch_lh+rh.mgz change
> between 0-200 , while this is 0-12175 for the Destrieux Atlas. These
> effects are also apparent in the ultimate results (parcellation.nii images,
> which I generate by using .mgz files). They are not aligned properly and
> their intensity is also erroneous. I suspect that we have a mistake in the
> above pipeline.
>
> *My questions are: *
> * 1) Is there simpler way to do this task? (For example, a simple addition
> to the recon-all function, etc.)*
> * 2) If not, what else should I do to be able to get the correct
> parcellations ? *
> *PS: I am a bit new to the FreeSurfer and MRI processing, so please accept
> my apologizes if this is a simple question... *
>   Thank you in advance and best regards.
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