Good Afternoon Freesurfers,

I am running a seed-based connectivity for one individual subject. The seed is in the L_parahippocampus. I have followed the steps outlined in FSFast walkthrough. Below is a list of my commands. Mind you that I was trying to keep my analysis as simple as possible before delving deeper into it. I have a question on the sig.nii.gz output. Please see at the end.

preproc-sess -s taha_brain -fwhm 0 -surface self lhrh -mni305-2mm -fsd resting_scans -per-run

fcseed-config -segid 1016 -fcname L_parahipp -fsd resting_scans -mean -cfg mean.L_parahipp.config -overwrite -fillthresh 1

fcseed-sess -s taha_brain -cfg mean.L_parahipp.config

mkanalysis-sess -analysis L_parahipp_seed.surf.lh -surface self lh -fwhm 0 -notask -taskreg L_parahipp 1 -fsd resting_scans -TR 0.555 -mcextreg -polyfit 2 -per-run

selxavg3-sess -s taha_brain -a L_parahipp_seed.surf.lh

Output files /home/tabdullah/Project/Sess01/fsd/L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz

amongst others

Is there a way to convert the volume to a surface and then extract per vertex the sig value? I used tmri_vol2surf see below:

mri_vol2surf --mov ./sig.nii.gz --reg /home/tabdullah/resting_state_1/taha_brain/resting_scans/001/register.dof6.dat --trgsubject taha_brain --interp nearest --projfrac 0.5 --hemi lh --o /home/tabdullah/sig.mgh --noreshape --cortex

I tried using mris_convert -c

mris_convert -c ./sig.mgh /usr/local/freesurfer/subjects/taha_brain/surf/lh.white sig.asc

The last column is all zeros. I am not entirely sure what I am doing wrong here, it is probably somewhere in the last two commands. Possibly using mri_segstats or mri_read.m? Any help would be greatly appreciated. Apologize in advance for the long email.

Taha Abdullah

Department of Physiology

Northwestern University Feinberg School of Medicine

Masters of Science Physiology and Biophysics, Georgetown University 2015

Work: (312)-503-0413