Re: [Freesurfer] Monte Carlo Simulation in Qdec
Thank you so much for your help. The fwhm of 0 and 5 both work. I was wondering if you knew of any references or sites I could reference to justify this level of smoothing. Tara - Original Message - From: "Marie Schaer" To: "Douglas N Greve" Cc: "Nick Schmansky" , freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, September 4, 2013 10:36:14 AM Subject: Re: [Freesurfer] Monte Carlo Simulation in Qdec Hi Tara, You can try with fwhm=0 as Doug suggested, or 5 if it works. I'm still trying to see whether the level of fwhm could be modified in qdec so that you can input your own level (e.g. 1 or 2, instead of the specified 0-5-10-15-20-25). Nick, Do you know if there is a keyword that can be changed in .Qdecr to add different smoothing values to the FWHM menu in Qdec? Thanks! Marie On Sep 4, 2013, at 8:03 AM, Douglas N Greve wrote: > > Hi Tara, The problem is that the lGI is already very smooth and then it > gets smoothed again. This causes the total smoothness level to go beyond > what has been done for the simulation. Try using fwhm=0. > > doug > > > On 09/04/2013 09:48 AM, Tara Ann Miskovich wrote: >> Hello, >> >> I am conducting group analyses with LGI data in qdec, and I am having an >> issue with the monte carlo simulation I am hoping to get help with. >> >> Under design I leave the Smoothing (FWHM) at 10, and when I try to run the >> monte carlo simulation after running the analysis I get this error: Error in >> Monte Carlo simulation: Error running mri_surfcluster. Plus in the terminal >> I get an error: mri_surfclusterfwhm.dat: 37.226284, rounded to 38 Error: >> fwhm out-of-range (< 1 or > 30)! >> >> Should I be using fwhm0 for LGI data? >> >> Thank you for your help! >> >> Tara >> ___ >> 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error when running mris_anatomical_stats on a label
Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t sub200/surf/lh.pial_lgi -f sub200/stats/lh.precuneus_lgi.stats sub200 lh This is the output: limiting computations to label sub200/label/lh.trait_precuneus.label. using thickness file sub200/surf/lh.pial_lgi. reading volume /media/LGI/LGI/sub200/mri/wm.mgz... reading input surface /media/LGI/LGI/sub200/surf/lh.white... reading input pial surface /media/LGI/LGI/sub200/surf/lh.pial... reading input white surface /media/LGI/LGI/sub200/surf/lh.white... Segmentation fault (core dumped) Thank you for the help! Tara ___ 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.
Re: [Freesurfer] aparcstats2table for manually drawn ROIs
Hi Jack,
You can specify the .stats file created. Here is an example from the script I
use.
Anyone, correct me if this is wrong!
Tara
mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f
${subject}/stats/lh_frontal_surface.stats ${subject} lh pial
aparcstats2table --hemi lh \
--subjects sub1 sub2 sub3 \
--meas thickness \
--parc lh_frontal_surface \
--tablefile lh.frontal_thickness.stats.txt
- Original Message -
From: "Jackie Lam"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, October 3, 2013 12:51:21 PM
Subject: [Freesurfer] aparcstats2table for manually drawn ROIs
Hi there,
So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn
my ROIs, used mris_anatomical_stats to create a .stats files for each subject
from my hand drawn ROIs and now I want to use aparcstats2table to gather the
thicknesses from all my subjects Is there an option to gather stats from a
particular .stats file rather than from just the two parcellation atlases? I
think there is something similar in asegstats2table (--stats=lh.xxx.stats), but
is there something like that for aparcstats2table?
Many thanks,
Jack
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[Freesurfer] Error when running mris_anatomical_stats
Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t sub200/surf/lh.pial_lgi -f sub200/stats/lh.precuneus_lgi.stats sub200 lh This is the output: limiting computations to label sub200/label/lh.trait_precuneus.label. using thickness file sub200/surf/lh.pial_lgi. reading volume /media/LGI/LGI/sub200/mri/wm.mgz... reading input surface /media/LGI/LGI/sub200/surf/lh.white... reading input pial surface /media/LGI/LGI/sub200/surf/lh.pial... reading input white surface /media/LGI/LGI/sub200/surf/lh.white... Segmentation fault (core dumped) Thank you for the help! Tara ___ 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.
[Freesurfer] Cluster Annotation file and mris_anatomical_stats
Hi Everyone,
I am having trouble running mris_anatomical_stats on an annotation file
produced from my group analysis in qdec.
This is my code, but it seems to want to pull the annotation file from the
subject/label directory. Should I just make a copy into everyone's label file?
mris_anatomical_stats -a
qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot -t
${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
${subject} lh
Thank you!
Tara
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Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Thank you Doug, this did work. However, for every subject I get this line
repeated over and over before it outputs the stats. I still get a stats file
that seems to make sense but I am not sure if this is an issue.
MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
in_array_size=136201
annot file:
./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
Thank you for the help!
Tara
- Original Message -
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, October 4, 2013 6:29:49 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
This may sound incredibly trivial, but try putting a "./" infront of
qdec, ie, "-a ./qdec/..."
doug
On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
> Hi Everyone,
>
> I am having trouble running mris_anatomical_stats on an annotation file
> produced from my group analysis in qdec.
>
> This is my code, but it seems to want to pull the annotation file from the
> subject/label directory. Should I just make a copy into everyone's label file?
>
> mris_anatomical_stats -a
> qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
> -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
> ${subject} lh
>
> Thank you!
> Tara
> ___
> 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/
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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
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Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
I see, could you help me go about this. I have not been able to figure out how
to do this with an annotation file. And I believe I already mapped my lgi to
fsaverage space before group level through recon-all -qcache. Is this what you
mean?
Thank you again for the help!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, October 7, 2013 1:59:37 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Oh, you'll need to map the annotation into the individual space, or (and
probably better), map your lgi into fsaverage space.
doug
On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
> Thank you Doug, this did work. However, for every subject I get this line
> repeated over and over before it outputs the stats. I still get a stats file
> that seems to make sense but I am not sure if this is an issue.
>
> MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
> in_array_size=136201
> annot file:
> ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
>
> Thank you for the help!
> Tara
>
>
>
> - Original Message -
> From: "Douglas N Greve"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, October 4, 2013 6:29:49 PM
> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>
>
> This may sound incredibly trivial, but try putting a "./" infront of
> qdec, ie, "-a ./qdec/..."
>
> doug
>
>
> On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
>> Hi Everyone,
>>
>> I am having trouble running mris_anatomical_stats on an annotation file
>> produced from my group analysis in qdec.
>>
>> This is my code, but it seems to want to pull the annotation file from the
>> subject/label directory. Should I just make a copy into everyone's label
>> file?
>>
>> mris_anatomical_stats -a
>> qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
>> -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
>> ${subject} lh
>>
>> Thank you!
>> Tara
>> ___
>> 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/
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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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
I did. This is what I get from my group analysis in the folder. I didn't find
the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vertex.mgh
F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh
gamma.mgh mc-z.abs.th13.sig.cluster.summary
gammavar.mgh mc-z.abs.th13.sig.ocn.annot
Thank you again for the help!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 10:48:10 AM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you need?
doug
On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
> I see, could you help me go about this. I have not been able to figure out
> how to do this with an annotation file. And I believe I already mapped my lgi
> to fsaverage space before group level through recon-all -qcache. Is this what
> you mean?
>
> Thank you again for the help!
> Tara
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Tara Ann Miskovich"
> Cc: freesurfer@nmr.mgh.harvard.edu
> Sent: Monday, October 7, 2013 1:59:37 PM
> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>
>
> Oh, you'll need to map the annotation into the individual space, or (and
> probably better), map your lgi into fsaverage space.
>
> doug
>
>
>
>
> On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
>> Thank you Doug, this did work. However, for every subject I get this line
>> repeated over and over before it outputs the stats. I still get a stats file
>> that seems to make sense but I am not sure if this is an issue.
>>
>> MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
>> in_array_size=136201
>> annot file:
>> ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
>>
>> Thank you for the help!
>> Tara
>>
>>
>>
>> - Original Message -
>> From: "Douglas N Greve"
>> To: freesurfer@nmr.mgh.harvard.edu
>> Sent: Friday, October 4, 2013 6:29:49 PM
>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>>
>>
>> This may sound incredibly trivial, but try putting a "./" infront of
>> qdec, ie, "-a ./qdec/..."
>>
>> doug
>>
>>
>> On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
>>> Hi Everyone,
>>>
>>> I am having trouble running mris_anatomical_stats on an annotation file
>>> produced from my group analysis in qdec.
>>>
>>> This is my code, but it seems to want to pull the annotation file from the
>>> subject/label directory. Should I just make a copy into everyone's label
>>> file?
>>>
>>> mris_anatomical_stats -a
>>> qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
>>> -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
>>> ${subject} lh
>>>
>>> Thank you!
>>> Tara
>>> ___
>>> 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/
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] Cluster Annotation file and mris_anatomical_stats
version 5.0.0
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 1:57:35 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
what version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
> I did. This is what I get from my group analysis in the folder. I didn't find
> the ocn.dat file. Is there something I need to do in Qdec to produce it?
>
> C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
> cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vertex.mgh
> F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh
> gamma.mgh mc-z.abs.th13.sig.cluster.summary
> gammavar.mgh mc-z.abs.th13.sig.ocn.annot
>
> Thank you again for the help!
> Tara
>
> ----- Original Message -
> From: "Douglas N Greve"
> To: "Tara Ann Miskovich"
> Cc: freesurfer@nmr.mgh.harvard.edu
> Sent: Tuesday, October 8, 2013 10:48:10 AM
> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>
>
> Did you generate the annotation from a qdec analysis of lgi? If so, then
> there should be a file already there called something like
> mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
> each cluster. The value will be the mean lgi for that subject and
> cluster. Is this what you need?
>
> doug
>
>
>
>
> On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote:
>> I see, could you help me go about this. I have not been able to figure out
>> how to do this with an annotation file. And I believe I already mapped my
>> lgi to fsaverage space before group level through recon-all -qcache. Is this
>> what you mean?
>>
>> Thank you again for the help!
>> Tara
>>
>> - Original Message -
>> From: "Douglas N Greve"
>> To: "Tara Ann Miskovich"
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Sent: Monday, October 7, 2013 1:59:37 PM
>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>>
>>
>> Oh, you'll need to map the annotation into the individual space, or (and
>> probably better), map your lgi into fsaverage space.
>>
>> doug
>>
>>
>>
>>
>> On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote:
>>> Thank you Doug, this did work. However, for every subject I get this line
>>> repeated over and over before it outputs the stats. I still get a stats
>>> file that seems to make sense but I am not sure if this is an issue.
>>>
>>> MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=,
>>> in_array_size=136201
>>>annot file:
>>> ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot
>>>
>>> Thank you for the help!
>>> Tara
>>>
>>>
>>>
>>> - Original Message -
>>> From: "Douglas N Greve"
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Sent: Friday, October 4, 2013 6:29:49 PM
>>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
>>>
>>>
>>> This may sound incredibly trivial, but try putting a "./" infront of
>>> qdec, ie, "-a ./qdec/..."
>>>
>>> doug
>>>
>>>
>>> On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
>>>> Hi Everyone,
>>>>
>>>> I am having trouble running mris_anatomical_stats on an annotation file
>>>> produced from my group analysis in qdec.
>>>>
>>>> This is my code, but it seems to want to pull the annotation file from the
>>>> subject/label directory. Should I just make a copy into everyone's label
>>>> file?
>>>>
>>>> mris_anatomical_stats -a
>>>> qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot
>>>> -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats
>>>> ${subject} lh
>>>>
>>>> Thank you!
>>>> Tara
>>>> ___
>>>> 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
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Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
Thank you so much! Tara - Original Message - From: "Douglas N Greve" To: "Tara Ann Miskovich" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 8, 2013 2:15:33 PM Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats OK, the feature that computes that file was added after that. One thing you can do is to download 5.3 and use 5.3 to do your stats. There should not be any difference. Alternatively, you can run mri_segstats yourself, something like mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf mc-z.abs.th13.sig.ocn.dat --excludeid 0 where y.mgh is the file created by qdec to be used in the glm analysis doug On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote: > version 5.0.0 > > - Original Message - > From: "Douglas N Greve" > To: "Tara Ann Miskovich" > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, October 8, 2013 1:57:35 PM > Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats > > > what version of FS are you using? > > On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote: >> I did. This is what I get from my group analysis in the folder. I didn't >> find the ocn.dat file. Is there something I need to do in Qdec to produce it? >> >> C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh >> cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vertex.mgh >> F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh >> gamma.mgh mc-z.abs.th13.sig.cluster.summary >> gammavar.mgh mc-z.abs.th13.sig.ocn.annot >> >> Thank you again for the help! >> Tara >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Tara Ann Miskovich" >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, October 8, 2013 10:48:10 AM >> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >> >> >> Did you generate the annotation from a qdec analysis of lgi? If so, then >> there should be a file already there called something like >> mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for >> each cluster. The value will be the mean lgi for that subject and >> cluster. Is this what you need? >> >> doug >> >> >> >> >> On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote: >>> I see, could you help me go about this. I have not been able to figure out >>> how to do this with an annotation file. And I believe I already mapped my >>> lgi to fsaverage space before group level through recon-all -qcache. Is >>> this what you mean? >>> >>> Thank you again for the help! >>> Tara >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Tara Ann Miskovich" >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Monday, October 7, 2013 1:59:37 PM >>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >>> >>> >>> Oh, you'll need to map the annotation into the individual space, or (and >>> probably better), map your lgi into fsaverage space. >>> >>> doug >>> >>> >>> >>> >>> On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote: >>>> Thank you Doug, this did work. However, for every subject I get this line >>>> repeated over and over before it outputs the stats. I still get a stats >>>> file that seems to make sense but I am not sure if this is an issue. >>>> >>>> MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=0000, >>>> in_array_size=136201 >>>> annot file: >>>> ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot >>>> >>>> Thank you for the help! >>>> Tara >>>> >>>> >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Sent: Friday, October 4, 2013 6:29:49 PM >>>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >>>> >>>> >>>> This may sound incredibly trivial, but try putting a "./" infront of >>>> qdec, ie, "-a ./qdec/..." >>>> >>>> doug >>>> >>>> >>>> On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote: >>>>> Hi Everyone, >>>>> >>>>> I am havi
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
opps sorry one last question. Will segstats get me LGI estimates of the pial surface? Tara - Original Message - From: "Douglas N Greve" To: "Tara Ann Miskovich" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 8, 2013 2:15:33 PM Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats OK, the feature that computes that file was added after that. One thing you can do is to download 5.3 and use 5.3 to do your stats. There should not be any difference. Alternatively, you can run mri_segstats yourself, something like mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf mc-z.abs.th13.sig.ocn.dat --excludeid 0 where y.mgh is the file created by qdec to be used in the glm analysis doug On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote: > version 5.0.0 > > - Original Message - > From: "Douglas N Greve" > To: "Tara Ann Miskovich" > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, October 8, 2013 1:57:35 PM > Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats > > > what version of FS are you using? > > On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote: >> I did. This is what I get from my group analysis in the folder. I didn't >> find the ocn.dat file. Is there something I need to do in Qdec to produce it? >> >> C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh >> cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vertex.mgh >> F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh >> gamma.mgh mc-z.abs.th13.sig.cluster.summary >> gammavar.mgh mc-z.abs.th13.sig.ocn.annot >> >> Thank you again for the help! >> Tara >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Tara Ann Miskovich" >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, October 8, 2013 10:48:10 AM >> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >> >> >> Did you generate the annotation from a qdec analysis of lgi? If so, then >> there should be a file already there called something like >> mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for >> each cluster. The value will be the mean lgi for that subject and >> cluster. Is this what you need? >> >> doug >> >> >> >> >> On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote: >>> I see, could you help me go about this. I have not been able to figure out >>> how to do this with an annotation file. And I believe I already mapped my >>> lgi to fsaverage space before group level through recon-all -qcache. Is >>> this what you mean? >>> >>> Thank you again for the help! >>> Tara >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Tara Ann Miskovich" >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Monday, October 7, 2013 1:59:37 PM >>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >>> >>> >>> Oh, you'll need to map the annotation into the individual space, or (and >>> probably better), map your lgi into fsaverage space. >>> >>> doug >>> >>> >>> >>> >>> On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote: >>>> Thank you Doug, this did work. However, for every subject I get this line >>>> repeated over and over before it outputs the stats. I still get a stats >>>> file that seems to make sense but I am not sure if this is an issue. >>>> >>>> MRISreadAnnotationIntoArray: vertex index out of range: 163841 i=0000, >>>> in_array_size=136201 >>>> annot file: >>>> ./qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-trait-Cor/mc-z.abs.th13.sig.ocn.annot >>>> >>>> Thank you for the help! >>>> Tara >>>> >>>> >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Sent: Friday, October 4, 2013 6:29:49 PM >>>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >>>> >>>> >>>> This may sound incredibly trivial, but try putting a "./" infront of >>>> qdec, ie, "-a ./qdec/..." >>>> >>>> doug >>>> >>>> >>>> On 10/04/2013 03:42 PM, Tara Ann Miskovich w
Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
I see. Thank you so much for everything! Tara - Original Message - From: "Douglas N Greve" To: "Tara Ann Miskovich" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 8, 2013 2:42:36 PM Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats it gives you estimates of whatever you give it. If the y.mgh file are pial estimates, then that is what you will get doug On 10/08/2013 03:40 PM, Tara Ann Miskovich wrote: > opps sorry one last question. Will segstats get me LGI estimates of the pial > surface? > > Tara > > - Original Message ----- > From: "Douglas N Greve" > To: "Tara Ann Miskovich" > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, October 8, 2013 2:15:33 PM > Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats > > > OK, the feature that computes that file was added after that. One thing > you can do is to download 5.3 and use 5.3 to do your stats. There should > not be any difference. Alternatively, you can run mri_segstats yourself, > something like > > mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf > mc-z.abs.th13.sig.ocn.dat --excludeid 0 > > where y.mgh is the file created by qdec to be used in the glm analysis > > doug > > On 10/08/2013 03:01 PM, Tara Ann Miskovich wrote: >> version 5.0.0 >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Tara Ann Miskovich" >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, October 8, 2013 1:57:35 PM >> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >> >> >> what version of FS are you using? >> >> On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote: >>> I did. This is what I get from my group analysis in the folder. I didn't >>> find the ocn.dat file. Is there something I need to do in Qdec to produce >>> it? >>> >>> C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh >>> cnr.mgh mc-z.abs.th13.pdf.dat >>> mc-z.abs.th13.sig.vertex.mgh >>> F.mgh mc-z.abs.th13.sig.cluster.mgh sig.mgh >>> gamma.mgh mc-z.abs.th13.sig.cluster.summary >>> gammavar.mgh mc-z.abs.th13.sig.ocn.annot >>> >>> Thank you again for the help! >>> Tara >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Tara Ann Miskovich" >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Tuesday, October 8, 2013 10:48:10 AM >>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >>> >>> >>> Did you generate the annotation from a qdec analysis of lgi? If so, then >>> there should be a file already there called something like >>> mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for >>> each cluster. The value will be the mean lgi for that subject and >>> cluster. Is this what you need? >>> >>> doug >>> >>> >>> >>> >>> On 10/08/2013 09:04 AM, Tara Ann Miskovich wrote: >>>> I see, could you help me go about this. I have not been able to figure out >>>> how to do this with an annotation file. And I believe I already mapped my >>>> lgi to fsaverage space before group level through recon-all -qcache. Is >>>> this what you mean? >>>> >>>> Thank you again for the help! >>>> Tara >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: "Tara Ann Miskovich" >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Sent: Monday, October 7, 2013 1:59:37 PM >>>> Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats >>>> >>>> >>>> Oh, you'll need to map the annotation into the individual space, or (and >>>> probably better), map your lgi into fsaverage space. >>>> >>>> doug >>>> >>>> >>>> >>>> >>>> On 10/07/2013 02:18 PM, Tara Ann Miskovich wrote: >>>>> Thank you Doug, this did work. However, for every subject I get this line >>>>> repeated over and over before it outputs the stats. I still get a stats >>>>> file that seems to make sense but I am not sure if this is an issue. >>>>> >>>>> MRISreadAnnotationIntoArray: vertex index out of range: 163841 >>>>> i=, in_arra
[Freesurfer] sulci depth in table
Hello,
I am extracting sulci depth using the following
mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc
Do you know how I could put this into aparcstats2table?
Thank you,
Tara
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Re: [Freesurfer] sulci depth in table
I see thank you, and what would I use as the measure? Because for
asegstats2table I chose between volume and mean correct? Sorry a bit new at
this.
Tara
- Original Message -
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, November 8, 2013 1:00:18 PM
Subject: Re: [Freesurfer] sulci depth in table
If you are using mri_segstats then you should use asegstats2table
doug
On 11/08/2013 11:35 AM, Tara Ann Miskovich wrote:
> Hello,
>
> I am extracting sulci depth using the following
>
> mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc
>
> Do you know how I could put this into aparcstats2table?
>
> Thank you,
>
> Tara
>
> ___
> 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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] Monte Carlo Simulation in Qdec
Hello, I am conducting group analyses with LGI data in qdec, and I am having an issue with the monte carlo simulation I am hoping to get help with. Under design I leave the Smoothing (FWHM) at 10, and when I try to run the monte carlo simulation after running the analysis I get this error: Error in Monte Carlo simulation: Error running mri_surfcluster. Plus in the terminal I get an error: mri_surfclusterfwhm.dat: 37.226284, rounded to 38 Error: fwhm out-of-range (< 1 or > 30)! Should I be using fwhm0 for LGI data? Thank you for your help! Tara ___ 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.
[Freesurfer] Output mris_anatomical_stats into table for spreadsheet
Hello everyone, I am trying to gather the curvature (of a frontal ROI created through mri_mergelabels) through mris_anatomical_stats using the following mris_anatomical_stats -l 1220/label/lh.frontalmerge.label -f frontal_table 1220 lh pial The table produced doesn't upload well into a spreadsheet (measurements all in one cell). Does anyone know how to make a table that can be uploaded into a spreadsheet? Thanks! Tara ___ 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.
[Freesurfer] Freesurfer Surface based ROI to AFNI?
Hi all, I am wondering if any one has any experience with converting a freesurfer surface based ROI created in QDEC into a format I could use on functional data in afni. Thank you, Tara ___ 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.
Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Thank you so much for your help Paul! I was wondering if I could get a little
more specific help with the .ctab file. Would I just add my ROI to the existing
FreesurferColorLUT.txt (named something different of course) or would I start a
new one from scratch?
Thanks again!
Tara
- Original Message -
From: "Paul Beach"
To: "Freesurfer support list" , misko...@uwm.edu
Sent: Thursday, June 5, 2014 12:26:00 PM
Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Hi Tara,
I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.
The following will do the process into individual subject space
First :
mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj}
--regmethod surface --hemi hemisphere
Do this for as many labels as you have...
Then :
Create a color table file (.ctab file) for each hemisphere that contains your
ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The
first entry should be the Freesurfer defined medial wall, which you can get
from each subject's aparc.annot via mri_annotation2label.
Then create an annotation file using your .ctab file and your ROIs - one for
each hemisphere
mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab
hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \
--l hemi.FS_medial_wall.label \
--l hemi.ROI1.label \
--l hemi.ROI2.label \
--l hemi.ROI3.label \
...
Then create a segmentation file from the annotation file
mri_aparc2aseg --s {$subj} --annot
annotion_you_created_without_hemi_designation --o
segmentation_file_name+aseg.mgz
Then make a gmroi_vol file from which you can extract your ROIs
mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader
segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp orig/001.mgz
Copy the gmroi_vol to your subject's afni directory
Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you put
in depends on your .ctab file order. The first ROI would be 1001. Like the
ColorLUT, the first digit being '1' is typically for L. hemi, while '2' would
be for the R. hemi.
3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,)' -prefix
ROI_name.nii.gz
You can then do your AFNI-based analyses with your ROIs.
Hopefully that's all clear. Let me know if I can help in another way.
Cheers,
Paul
On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < misko...@uwm.edu > wrote:
Hi all,
I am wondering if any one has any experience with converting a freesurfer
surface based ROI created in QDEC into a format I could use on functional data
in afni.
Thank you,
Tara
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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.
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU Co gnitive and Ge riatric N eurology T eam ( CoGeNT )
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Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Thank you Paul that is very helpful, but I could use a little more specific
help.
A little more context: I ran a group vertexwise analysis with all my subjects
mapped to the fsaverage and traced my group cluster in QDEC and saved the
label. Now I would like to somehow get it into afni in the same space and use
it for some functional analyses.
I mapped the label to each individual subjects space, but the next step I am
running into issues.
I don't seem to see any medial wall in the aparc annotation. Plus I am not
familiar with the color table, I was just wondering what that would look like.
Any help from anyone would be much appreciated!
Tara
- Original Message -
From: "Paul Beach"
To: "Freesurfer support list" , misko...@uwm.edu
Sent: Thursday, June 5, 2014 12:26:00 PM
Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Hi Tara,
I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.
The following will do the process into individual subject space
First :
mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj}
--regmethod surface --hemi hemisphere
Do this for as many labels as you have...
Then :
Create a color table file (.ctab file) for each hemisphere that contains your
ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The
first entry should be the Freesurfer defined medial wall, which you can get
from each subject's aparc.annot via mri_annotation2label.
Then create an annotation file using your .ctab file and your ROIs - one for
each hemisphere
mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab
hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \
--l hemi.FS_medial_wall.label \
--l hemi.ROI1.label \
--l hemi.ROI2.label \
--l hemi.ROI3.label \
...
Then create a segmentation file from the annotation file
mri_aparc2aseg --s {$subj} --annot
annotion_you_created_without_hemi_designation --o
segmentation_file_name+aseg.mgz
Then make a gmroi_vol file from which you can extract your ROIs
mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader
segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp orig/001.mgz
Copy the gmroi_vol to your subject's afni directory
Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you put
in depends on your .ctab file order. The first ROI would be 1001. Like the
ColorLUT, the first digit being '1' is typically for L. hemi, while '2' would
be for the R. hemi.
3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,)' -prefix
ROI_name.nii.gz
You can then do your AFNI-based analyses with your ROIs.
Hopefully that's all clear. Let me know if I can help in another way.
Cheers,
Paul
On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < misko...@uwm.edu > wrote:
Hi all,
I am wondering if any one has any experience with converting a freesurfer
surface based ROI created in QDEC into a format I could use on functional data
in afni.
Thank you,
Tara
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--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU Co gnitive and Ge riatric N eurology T eam ( CoGeNT )
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Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Thank you Anthony for the help! I am hoping you don't mind if I ask some more
specific questions for this is pretty new for me.
First off this surface ROI was traced from group results displayed on the
fsaverage. Do I map the label to each individual subject and run the
@SUMA_Make_spec_FS for each subject or should I just run the script on the
label traced off of the fsaverage.
Again thanks for the help this is just all new!
Tara
- Original Message -
From: "Anthony Dick"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, June 9, 2014 10:28:52 AM
Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Hello all,
I believe Ziad Saad and friends have written AFNI/SUMA to make this
easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will
convert all the volume-space segmentation and parcellation files to be
readable in AFNI. Takes only a couple of minutes.
Run @SUMA_Make_Spec_FS -help to see the command line syntax. Look for
the relevant files in the SUMA folder. You can also edit the @SUMA
program to add any file you have newly created that is not a standard
freesurfer file.
Anthony
On 6/9/14, 11:15 AM, Tara Ann Miskovich wrote:
> Thank you Paul that is very helpful, but I could use a little more specific
> help.
>
> A little more context: I ran a group vertexwise analysis with all my subjects
> mapped to the fsaverage and traced my group cluster in QDEC and saved the
> label. Now I would like to somehow get it into afni in the same space and use
> it for some functional analyses.
>
> I mapped the label to each individual subjects space, but the next step I am
> running into issues.
>
> I don't seem to see any medial wall in the aparc annotation. Plus I am not
> familiar with the color table, I was just wondering what that would look like.
>
> Any help from anyone would be much appreciated!
>
> Tara
>
> - Original Message -
> From: "Paul Beach"
> To: "Freesurfer support list" ,
> misko...@uwm.edu
> Sent: Thursday, June 5, 2014 12:26:00 PM
> Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
>
>
> Hi Tara,
>
>
> I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.
>
>
> The following will do the process into individual subject space
>
>
> First :
> mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj}
> --regmethod surface --hemi hemisphere
>
>
> Do this for as many labels as you have...
>
>
> Then :
> Create a color table file (.ctab file) for each hemisphere that contains your
> ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The
> first entry should be the Freesurfer defined medial wall, which you can get
> from each subject's aparc.annot via mri_annotation2label.
>
>
> Then create an annotation file using your .ctab file and your ROIs - one for
> each hemisphere
>
>
> mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab
> hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \
>
> --l hemi.FS_medial_wall.label \
>
> --l hemi.ROI1.label \
> --l hemi.ROI2.label \
>
> --l hemi.ROI3.label \
>
> ...
>
>
> Then create a segmentation file from the annotation file
>
>
> mri_aparc2aseg --s {$subj} --annot
> annotion_you_created_without_hemi_designation --o
> segmentation_file_name+aseg.mgz
>
>
>
> Then make a gmroi_vol file from which you can extract your ROIs
>
>
>
> mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader
> segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp
> orig/001.mgz
>
>
> Copy the gmroi_vol to your subject's afni directory
>
>
> Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you
> put in depends on your .ctab file order. The first ROI would be 1001. Like
> the ColorLUT, the first digit being '1' is typically for L. hemi, while '2'
> would be for the R. hemi.
>
>
> 3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,)' -prefix
> ROI_name.nii.gz
>
>
>
>
>
> You can then do your AFNI-based analyses with your ROIs.
>
>
> Hopefully that's all clear. Let me know if I can help in another way.
>
>
>
>
> Cheers,
> Paul
>
>
>
>
>
> On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich < misko...@uwm.edu >
> wrote:
>
>
> Hi all,
>
> I am wondering if any one has any experience with converting a freesurfer
> surface based ROI created in QDEC into a format I could use on functional
> data in afni.
>
> Thank you,
>
> Tara
>
> ___
> Free
[Freesurfer] Qdec Annotation to Individual
Hello, I was hoping someone could help me map with mapping my annotation from my significant qdec clusters into each individual space. Thanks! Tara Tara A. Miskovich, B.A. Affective Neuroscience Laboratory Department of Psychology University of Wisconsin-Milwaukee 334 Garland Hall misko...@uwm.edu ___ 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.
Re: [Freesurfer] Qdec Annotation to Individual
Thank you for your response Doug. On my help it only goes up to example 5. I am trying to figure out how to do it without a subject1 since the annotation is in the qdec directory. Thanks - Original Message - From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 26, 2014 11:05:49 AM Subject: Re: [Freesurfer] Qdec Annotation to Individual You can use mri_surf2surf with the --sval-annot option. Run it with --help and look at example 6 doug On 06/26/2014 11:04 AM, Tara Ann Miskovich wrote: > Hello, > > I was hoping someone could help me map with mapping my annotation from my > significant qdec clusters into each individual space. > > Thanks! > > Tara > > > Tara A. Miskovich, B.A. > Affective Neuroscience Laboratory > Department of Psychology > University of Wisconsin-Milwaukee > 334 Garland Hall > misko...@uwm.edu > > > ___ > 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec Annotation to Individual
Thank you very much! Tara - Original Message - From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 26, 2014 11:37:40 AM Subject: Re: [Freesurfer] Qdec Annotation to Individual Try using this version of mri_surf2surf. I've also put example 6 below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf You can give it the full path to the input annotation doug 6. Convert the annotation for one subject to the surface of another mri_surf2surf --srcsubject subj1 --trgsubject subj2 --hemi lh \ --sval-annot $SUBJECTS_DIR/subj1/label/lh.aparc.annot \ --tval $SUBJECTS_DIR/subj2/label/lh.subj1.aparc.annot This will create $SUBJECTS_DIR/subj2/label/lh.subj1.aparc.annot. The --sval-annot flag will also change the map method to nnf so that the annot indices are not averaged. Note: 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. On 06/26/2014 12:34 PM, Tara Ann Miskovich wrote: > Thank you for your response Doug. On my help it only goes up to example 5. I > am trying to figure out how to do it without a subject1 since the annotation > is in the qdec directory. > > Thanks > > - Original Message - > From: "Douglas N Greve" > To: freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, June 26, 2014 11:05:49 AM > Subject: Re: [Freesurfer] Qdec Annotation to Individual > > > You can use mri_surf2surf with the --sval-annot option. Run it with > --help and look at example 6 > doug > > On 06/26/2014 11:04 AM, Tara Ann Miskovich wrote: >> Hello, >> >> I was hoping someone could help me map with mapping my annotation from my >> significant qdec clusters into each individual space. >> >> Thanks! >> >> Tara >> >> >> Tara A. Miskovich, B.A. >> Affective Neuroscience Laboratory >> Department of Psychology >> University of Wisconsin-Milwaukee >> 334 Garland Hall >> misko...@uwm.edu >> >> >> ___ >> 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec Annotation to Individual
One last question. What would I put as the source subject? Do I need something there? - Original Message - From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 26, 2014 11:37:40 AM Subject: Re: [Freesurfer] Qdec Annotation to Individual Try using this version of mri_surf2surf. I've also put example 6 below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf You can give it the full path to the input annotation doug 6. Convert the annotation for one subject to the surface of another mri_surf2surf --srcsubject subj1 --trgsubject subj2 --hemi lh \ --sval-annot $SUBJECTS_DIR/subj1/label/lh.aparc.annot \ --tval $SUBJECTS_DIR/subj2/label/lh.subj1.aparc.annot This will create $SUBJECTS_DIR/subj2/label/lh.subj1.aparc.annot. The --sval-annot flag will also change the map method to nnf so that the annot indices are not averaged. Note: 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. On 06/26/2014 12:34 PM, Tara Ann Miskovich wrote: > Thank you for your response Doug. On my help it only goes up to example 5. I > am trying to figure out how to do it without a subject1 since the annotation > is in the qdec directory. > > Thanks > > - Original Message - > From: "Douglas N Greve" > To: freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, June 26, 2014 11:05:49 AM > Subject: Re: [Freesurfer] Qdec Annotation to Individual > > > You can use mri_surf2surf with the --sval-annot option. Run it with > --help and look at example 6 > doug > > On 06/26/2014 11:04 AM, Tara Ann Miskovich wrote: >> Hello, >> >> I was hoping someone could help me map with mapping my annotation from my >> significant qdec clusters into each individual space. >> >> Thanks! >> >> Tara >> >> >> Tara A. Miskovich, B.A. >> Affective Neuroscience Laboratory >> Department of Psychology >> University of Wisconsin-Milwaukee >> 334 Garland Hall >> misko...@uwm.edu >> >> >> ___ >> 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question with QDEC annotations and mri_convert and mri_annotation2label
Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara ___ 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.
[Freesurfer] Question with QDEC annotations and mri_convert and mri_annotation2label
Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara ___ 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.
[Freesurfer] Help with QDEC Sig Cluster annotations and mri_convert and mri_annotation2label
Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
