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.