External Email - Use Caution Dear Dr Greve, thank you so much for answers to my questions. Regarding question 2, yes I meant leaving only columns I need, for instance I am interested in lobes. I ran these commands on my data
# mri_annotation2label --subject subject --hemi lh --lobesStrict lobes # mri_annotation2label --subject subject --hemi rh --lobesStrict lobes # mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \ # --volmask --o wmparc.lobes.mgz --ctxseg aparc+aseg.mgz \ # --annot lobes --base-offset 200 [--base-offset must be last arg] then mri_segstats and I got the final stats file which contain data for the lobes rois 3201 wm-lh-frontal-lobe 3203 wm-lh-cingulate-lobe 3204 wm-lh-occiptal-lobe 3205 wm-lh-temporal-lobe 3206 wm-lh-parietal-lobe 3207 wm-lh-insula-lobe 4201 wm-rh-frontal-lobe 4203 wm-rh-cingulate-lobe 4204 wm-rh-occiptal-lobe 4205 wm-rh-temporal-lobe 4206 wm-rh-parietal-lobe 4207 wm-rh-insula-lobe My question is can I revise the spreadsheet from the output of aparcstats2table or asegstats2table to keep the lobar ROIs above (8 columns) then feed that data to mri_glmfit? On 12/20/2022 12:22 PM, James Brown wrote: Dear Freesurfer experts, I have 2 questions about the command mri_glmfit and I appreciate your help. 1- Are there any settings or flags that can be used in mri_glmfit to restrict statistical comparison of surface based analysis to specific ROIs rather than whole brain analysis. I would like to show the difference on the brain surface in lobes rather than in sub lobar labels. You can create a mask or label and feed it into mri_glmfit with --mask or --label 2- I understand that the flag "--table" in command mri_glmfit allows for feeding spreadsheets instead of images. Can we restrict the number of columns in this spreadsheet to 8 columns for lobs (frontal, temporal, occipital and parietal) left and right? Also, is there any way to generate a statistical map from the spreadsheet statistics? Remove the columns you don't want? On Tue, Dec 20, 2022 at 12:22 PM James Brown <jb1979...@gmail.com> wrote: > Dear Freesurfer experts, > I have 2 questions about the command mri_glmfit and I appreciate your help. > 1- Are there any settings or flags that can be used in mri_glmfit to > restrict statistical comparison of surface based analysis to specific ROIs > rather than whole brain analysis. I would like to show the difference on > the brain surface in lobes rather than in sub lobar labels. > 2- I understand that the flag "--table" in command mri_glmfit allows for > feeding spreadsheets instead of images. Can we restrict the number of > columns in this spreadsheet to 8 columns for lobs (frontal, temporal, > occipital and parietal) left and right? Also, is there any way to generate > a statistical map from the spreadsheet statistics? > > Thank you and happy holidays :) > James > >
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