1 Jun
2021
1 Jun
'21
6:19 p.m.
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:
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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 <dgreve@mgh.harvard.edu mailto:dgreve@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:External Email - Use Caution 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 <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* 27 May 2021 21:05 *To:* Aldinhas De Freitas Ferreira, Francisca <francisca.ferreira.16@ucl.ac.uk> <mailto:francisca.ferreira.16@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! 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