I want to measure cortical thickness in 7 volume-defined ROIs (created in Marsbar). I followed the tutorial
http://freesurfer.net/fswiki/VolumeRoiCorticalThickness. When I want to visualize my surface-based ROI after mri_vol2surf, for some reason ROI 6 and 7 do not appear in tksurfer (and with segstats, no segmentation is found). FreeSurfer does not seem to give any error message:
$ mri_vol2surf --mov ~/Desktop/anita-vumc/7Rmidtempgyrus.nii --reg avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh.fsaverage.7Rmidtempgyrus.mgh --reshape
srcvol = /home/guest/Desktop/anita-vumc/7Rmidtempgyrus.nii
srcreg = avg152T1_to_fsaverage.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = 0.5
reshape = 1
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Reading surface /data1/projects/ysbrand-vumc/pddatabase-freesurfer/fsaverage/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 1
using old
2 0.1 0 1
using old
3 0.2 0 1
using old
4 0.3 0 1
using old
5 0.4 0 1
using old
6 0.5 0 1
using old
7 0.6 0 1
using old
8 0.7 0 1
using old
9 0.8 0 1
using old
10 0.9 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 21723
Reshaping 7 (nvertices = 163842)
Writing to rh.fsaverage.7Rmidtempgyrus.mgh
Dim: 23406 1 7