[Freesurfer] Gray to white matter signal intensity ratio (GWR)

Dear Freesurfer users, I have just read the paper of Salat et al 2011 "Hippocampal degeneration is associated with temporal and limbic gray matter/white matter tissue contrast in Alzheimer's disease". I wonder how we can calculate the Gray to white matter signal intensity ratio (GWR)? Is the

[Freesurfer] Crossing surfaces in parcellation in hippocampus?

Dear freesurfer users, I am a new user of Freesurfer. I have a question about the parcellation: in my data, I am checking the pial and white surfaces of brains. I have observed on my subjects that surfaces are crossing in the hippocampus. I don't understand why the pial and white matter surfac

[Freesurfer] surface group analysis design matrix question

Dear freesurfer users, I have a question about a design matrx. I have read all your explications about the FSDG file. But I am not sure I can construct the design which corresponds to my study! I have two groups: control and patients. I want to compare their cortical thickness. I have have one

[Freesurfer] Problem with covariates in design for surface based analysis

Dear Freesurfur users, I have a question about the design for a surface based analysis! I want to compare controls and patients. I have 5 covariates. One is a continous variable. The others are categorial variables (4 with 2 levels and 1 with 5 levels). I want to ajust my result with all of th

[Freesurfer] problem generate stats data tables

Dear freesurfer users, I have tried to run "generate stats data tables", but I have that error message: asegstats2table --common-segs --meas volume --tablefile /home/charlotte/TROISCITES/DATA/FREESURFER/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 10049 10053 10079

[Freesurfer] mri_glmfit problem with y option

Dear Freesurfer users, I have tried to run mri-glmfit but I have obtained the error message: ERROR: Option --y unknown I don't understand why! I have run that command line: mri_glmfit \ --y lh.test.thickness.10.mgh \ --fsgd test.fsgd dods\ --C group.diff.mtx \ --surf fsaverage lh \ --cortex \

[Freesurfer] Create summary images

Dear Freesurfer users, I would like to know if it is possible to quickly inspect subcortical structure segmentation quality on a large number of subjects. I have read a post on that topic but i am not sure I understand how to process. Could you give a command line to do that? Thanks a lot, Ch

[Freesurfer] Data check

Dear Freesurfer users, I would like to know what is the procedure to check the quality of the Freesurfer process on my subjects. I have more than 500 subjects. 1/ Have I to check each segmented region on by one for each subject? 2/ How can we check the quality of the surf process? Thanks a lot

[Freesurfer] White matter intensity normalisation

Dear Freesurfer users, I run FS on my 670 subjects. All the scans were acquired on a 1.5T Philips scan. I noticed that my values in the WM are near 100-110 but not exactly 110. I think it is a problem! Is it link to the 1.5T? How can I fix it? I joined my log file of QA tools: could you help me

[Freesurfer] question about fsaverage

Dear Freesurfer experts, I would like to know if it is necessary to have exactly the same number of subjects in my fsaverage and in my qdec.table.dat? If it is a problem how can I eliminate the subjects I don't study from the fsaverage? Thanks for all, Charlotte

[Freesurfer] FWHM smoothing for surface based

Dear Freesurfer users, I would like to know what is the level of smooth recommanded to use for surface-based group analysis? Thank you, All the best, Charlotte ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] longitudinal data check problem

Dear Freesurfer users, I try to visualize my longitudinal data for one subject whit the command line given in the freesurfer website: freeview -v 00049_T1/mri/norm.mgz -f 00049_T1/surf/lh.pial:edgecolor=red 00049_T1/surf/rh.pial:edgecolor=red 00049_T1/surf/lh.white:edgecolor=blue 00049_T1/surf