Hello again,

To calculate cortical thickness, I am running step-4 & 5 following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

So running step 4:

mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape

where S01_LP is my subject ID, it runs as follow:

srcsubject = S01_LP
srcval     = lh.thickness
srctype    = 
trgsubject = fsaverage
trgval     = lh.thickness.fsaverage.mgh
trgtype    = 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi    = lh
trghemi    = lh
frame      = 0
fwhm-in    = 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg /media/Storage/FTD_Data/S01_LP/surf/lh.sphere.reg
Loading source data
Reading target surface reg /media/Storage/FTD_Data/fsaverage/surf/lh.sphere.reg
Done
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (98973)
Reverse Loop had 7939 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
nTrg121 = 157350, nTrgMulti =  6492, MnTrgMultiHits = 2.22289
nSrc121 = 49582, nSrcLost =     0, nSrcMulti = 49391, MnSrcMultiHits = 2.47411
Saving target data
Reshaping 6 (nvertices = 163842)
Saving to lh.thickness.fsaverage.mgh

Next when I run step 5 as follow:

mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt

It runs as follows:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt 
sysname  Linux
hostname degas
machine  x86_64
user     sahil
UseRobust  0
Loading /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh
Loading lh.thickness.fsaverage.mgh
ERROR: dimension mismatch between input volume and seg
  input 27307 1 6
  seg   23406 1 7