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 buseurgen@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