Not easily. You can do something in matlab, eg,
aseg = MRIread('fsaverage/mri/aseg.mgz');
out = aseg;
out.vol = zeros(out.volsize);
ind = find(aseg.vol==17); % 17 = left hippo
out.vol(ind) = YourValueForLeftHippoFromTheGLMAnalysis;
% same thing for other ROIs
MRIwrite(out,'sig.aseg.mgz');
Then visualize on the fsaverage volume
On 6/1/2021 6:14 PM, Francisca Ferreira wrote:
External Email - Use Caution
I see, thanks. Is there a way in Freesurfer to obtain a visual
representation of these results- like in other modalities of group
analysis? (eg. surface based)
Many thanks
On Tue, 1 Jun 2021 at 17:44, Douglas N. Greve <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>> wrote:
There are not results to visualize, there is just a table. There
should be a sig table in the output folder
On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
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So so sorry to bother you again - hopefully the last time...
I have followed your suggestion and that has worked, having used
this command
mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd
dods \--C groupdiff.mtx \--glmdir aseg.glmdir
I am now trying to visualise the results according to FSwiki,
used this command
freeview -f
/usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50
-viewport 3d
I get the following error
ERROR: reading /usr/local/freesurfer/subjects
Read 0 bytes, expected 1
Read 0 bytes, expected 1
/freesurfer/subjects
MRISread failed
I wonder is this means there is something wrong with the GLM I
created or if it is something wrong with my Freeview?
Thanks a lot in advance!
Kind regards,
Francisca
------------------------------------------------------------------------
*From:* Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* 27 May 2021 21:05
*To:* Aldinhas De Freitas Ferreira, Francisca
<francisca.ferreira...@ucl.ac.uk>
<mailto:francisca.ferreira...@ucl.ac.uk>
*Subject:* Re: Freesurfer- subcortical group analysis
Hi Francisca, if you run asegstats2table on your group to create
a group table (subjects on the rows, structures on the columns,
each element being the structure volume for that subject), then
you can use mri_glmfit with the --table option (instead of --y).
You may want to correct for intracranial volume by adding --etiv
to the asegstats2table command.
doug
On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
External Email - Use Caution
Dear Dr Greve,
My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging
PhD student at the FIL in UCL. I have recently contacted Eugenio
Iglesias, who kindly pointed me in your direction. Sorry to
bother you, I have been working with Freesurfer and I was hoping
you would kindly give me your opinion?
I am looking to compare responders vs non responders to deep
brain stimulation of a subcortical structure called ventral
tegmental area. I ran recon-all, and thought Freesurfer could be
useful for this task as it now has a brainstem segmenting module
that I’ve installed.
I thought I could use brainstem or subcortical volumes/surfaces
to do the glm group analysis? (in my case regressing out age and
gender). It seems that all the options i found on mri_glm only
allow surface-based analysis? (the flags available being - -
cortex or - -non-cortex) is there any way around this?
I am sorry for any lack of background knowledge- which stems
from the fact that I am primarily a clinician...
I’d be most grateful for any suggestions!
Kind regards,
Francisca
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