Dear Freesurfers, I have two questions:
1) In the last stage of the recon-all -s <subj> -localGI analysis, local gyrification index values are calculated at each pial vertices. Is there any way (command?) to extract *vertex-wise local gyrification index values* (of individual subjects) *before running GLM analysis in Qdec*? GLM analysis is not suitable for my study (single-case), so I need to extract values for each subject and use them for my own statistical analysis. 2) As far as I know we can extract *parcel-wise lGI* values using the following command: mri_segstats --annot *subjID* lh aparc \ --i $SUBJECTS_DIR/*subjID*/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.stats Running this command provides "Intensity Mean, Intensity STD, Intensity Max, Intensity Min, Intensity Range" values for each parcellated area. Can you explain these values and what they mean? Thanks, -Buse On 5 November 2017 at 19:54, Buse Merve Ürgen <buseur...@gmail.com> wrote: > Dear Freesurfer developers, > > I would like to run Local Gyrification Index analysis for a group of > healthy controls and a single patient. After running recon-all -s <subj> > -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the > last stage of this analysis, local gyrification index values are calculated > at each pial vertices. > > In the wiki, it is said that the next process should be done in qdec, but > since I have only one patient, GLM analysis would not be suitable. Thus, I > would like to get the LGI values of each subject as e.g. text files (like > stats files for curvature, thickness, gm volume), and use them for my own > analysis (not in qdec). I know that we can get parcel-wise anaysis values > using this command: > mri_segstats --annot CASE lh aparc \ > > --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \ > > --sum lh.aparc.pial_lgi.stats > > But I would like to use vertex-wise analysis values for my won analysis. > Is it possible? Can I learn the command I need to use to get these values > for each subject? > > Thank you, > Buse > > -- > > Buse > Urgen > > -- Buse M. Ürgen Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center Bilkent University Ankara, 06800 Turkey
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