: 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
> Succ
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 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
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,
>>
>>
cts/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 qualifie
"
> 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 :
>
>>
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
.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,
onents.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
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 corre
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 MN
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 co
ich
> 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: Thom
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 varia
mas
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 tha
nks 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
>> FreeSurf
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 ver
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
> <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
> 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
&g
bellum 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,
>>
f6.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 wro
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
c
,
> 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 --
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
ew 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
>
>
>
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
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
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
://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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https
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, 2
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 sci
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
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 t
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
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
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_cho
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 "subjec
cify 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.
certain projects.
Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.
Deadline: 1st May, 2014
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The information in this e
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?
Than
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 duplicat
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
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
> netwo
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 se
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
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 in
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/Yeo201
u 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.
>
>
>
>
>
>
>
> Excus
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
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 qui
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
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.
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,
ial 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
//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:
>
> Cho
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,
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
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 suf
ed 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.
>>&g
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
> __
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
> ___
> Freesur
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
>&g
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
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.
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/aver
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,
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 th
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
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 --trgsubje
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
gt; 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
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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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
ith 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:
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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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, Che
_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 netw
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, M
.
>
>
> 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 ne
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
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-le
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/GS
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 T
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
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
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
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 expe
e 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
>&g
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
m
> 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,
>>
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 wrot
e 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
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 dongnan
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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
wro
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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/yoursubje
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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 su
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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/lab
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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 Sa
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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 aut
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