Hi Doug and the Freesurfers,
Thanks for your help. I have 2 questions.:
1) I did the retinotopy analysis on the fsaverage surface as you suggested
below and then ran isxconcat-sess for my eccen and polar data:
e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf
sessid -o group_polar_lh
but how do you do this for the fieldsign analysis, since the cess.nii
and other files don't exist?
2) So when trying to run a group mri_glmfit on the polar and eccen maps
with:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh
--glmdir group_eccen_lh.wls --nii.gz
I got an error, because I have two ces.nii.gz and cesvar.nii.gz files each.
I am not sure how this happened. I only have one run each of polar and
wedge data. What may have generated these two files and which one do I use?
Thanks.
Michelle
On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> wrote:
> When you run preproc-sess use -surface fsaverage lhrh instead of -surface
> self lhrh. Then create a new analysis with the same parameters, except use
> -surface fsaverage lh instead of -surface self lh.
> doug
>
> Michelle Umali wrote:
>
>> Hi Doug,
>> I'm a little confused as to how to assign functional data to the fsaverage
>> space.
>> 1) Do you mean just change each subject's subjectname file to fsaverage
>> and then do the same thing as before for each person?
>> 2) Also, when I specify the analysis do I change -rtopy.self.lh to
>> rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name?
>>
>> e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy
>> 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force
>>
>> then the same for selxavg3-sess and fieldsign-sess
>>
>> and then isxconcat-sess would be:
>> isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh
>>
>>
>> Thanks.
>> Michelle
>>
>> On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>>
>> wrote:
>>
>> If you want to combine across subjects, then you need to run the
>> analysis on fsaverage (ie, rerun preproc-sess, create a new
>> analysis, run selxavg3-sess, and then isxconcat-sess).
>> doug
>>
>> Michelle Umali wrote:
>>
>> Dear Freesurfers,
>> I've generated individual polar, eccentricity, and fieldsign
>> maps for each of my subjects. I would like to generate group
>> average maps of these that I can visualize on the fsaverage brain.
>>
>> When I ran:
>> isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh
>>
>> I got:
>> ERROR: analysis space is self surface, not supported
>>
>> How do I do a group average for the 3 different maps?
>>
>> Thanks.
>> Michelle
>>
>> For each person I ran recon-all and flattened occipital patches.
>> Then:
>> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2
>> -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold
>> -force
>> mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2
>> -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold
>> -force
>>
>> preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd
>> bold -force
>>
>> selxavg3-sess -a rtopy.self.lh -s sjXX -force
>> selxavg3-sess -a rtopy.self.rh -s sjXX -force
>>
>> fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX
>> fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX
>>
>> ------------------------------**------------------------------**
>> ------------
>>
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>>
>> -- Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>
>> >
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>> <tel:617-726-7422>
>>
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>>
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>> >
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>>
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>> >
>>
>>
>>
>>
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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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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