On Thu, Oct 20, 2011 at 11:20 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Michelle Umali wrote:

Hi Doug,

Thank you for your help with this. So when I looked at the maps, two issues arose.

1) The fieldsign map looks like it needs lots of smoothing. When I ran the individual subjects on the surface, I smoothed by 20 during fieldsign-sess. Is it still appropriate/can one smooth at the mri_fieldsign step below?

Yes, the smoothing applied during the individual fieldsign creations does not apply to the group.

2)Results ended up on the lateral side and way anterior from the occipital lobe. Do I perform a separate registration between the individual subject and fsaverage somewhere along the line? Is this because I ran the individual subject analyses on a flattened fsaverage occipital patch and not on lh.sphere?

The individuals were run on the full fsaverage surface. The field sign created at the individual level is not used at all in the group analysis. There is not any additional registration that you should use. Try the smoothing in mri_fieldsign (--fwhm); if that does not fix the problem, send me a snapshot.

doug

Thanks!
Michelle

On Wed, Oct 19, 2011 at 7:34 PM, Michelle Umali <mumali01@gmail.com <mailto:mumali01@gmail.com>> wrote:

Hi Doug,
Two problems happened (I'm attaching a picture).
1) The fieldsign map looks like it needs lots of smoothing. When
I ran the individual subjects on the surface, I smoothed by 20
during fieldsign-sess. Is it still appropriate/can one smooth at
the mri_fieldsign step below?

2)Results ended up on the lateral side and way anterior from the
occipital lobe. Do I perform a separate registration between the
individual subject and fsaverage somewhere along the line? Is
this because I ran the individual subject analyses on a flattened
fsaverage occipital patch and not on lh.sphere?

Thanks!
Michelle

On Wed, Oct 19, 2011 at 5:30 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Hi Michelle, try this:

isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o
retgroup
cd retgroup/rtopy.fsaverage.lh

mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real
--surface fsaverage lh
mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag
--surface fsaverage lh
mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real
--surface fsaverage lh
mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag
--surface fsaverage lh

mri_fieldsign --fs lh.fieldsign.mgh \
--eccen eccen/glm.real/osgm/gamma.mgh
eccen/glm.imag/osgm/gamma.mgh \
--polar polar/glm.real/osgm/gamma.mgh
polar/glm.imag/osgm/gamma.mgh \
--s fsaverage --hemi lh --sphere --old

tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh
-fthresh .5

Michelle Umali wrote:

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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@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
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@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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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
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Phone Number: 617-724-2358 <tel:617-724-2358> Fax:
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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MGH-NMR Center
greve@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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