Thank you very much.
Here is the output.
surface registration and labeling (svreg)
This is the main program for surface registration. First, the surface is
smoothed to create a multiresolution representation of the surface. An
initial registration is performed by aligning the 3D coordinates of this
smoothed surface. This is followed by p-harmonic mapping to a square and
curvature-based registration.
For more information, please see http://brainsuite.org
Authored by Anand A. Joshi, Signal and Image Processing Institute
Department of Electrical Engineering, Viterbi School of Engineering, USC
usage: svreg_label_surf_hemi.sh [subject fileprefix] [atlas fileprefix]
[hemi] [flags]
required input:
subject fileprefix path and filename prefix of the subject’s output
from BrainSuite’s Cortical Surface Extraction
Sequence
atlas fileprefix path and filename prefix of atlas files and labels
to which the subject will be registered
hemi the hemisphere to refine; either left or right
optional flags:
-v# Controls the verbosity of output messages (# is 0, 1, or 2)
-t display timestamps along with output messages
Here is one of the errors i am getting from the run..
Using Executable /Applications/BrainSuite18a/svreg/bin/warp_points_mac
A matrix with a negative or zero determinant was encountered. (AIR_NON_POSITIVE_DETERMINANT_ERROR)
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:~/study/BS_SPGR/A11/A11.svreg.tmp/A11.target.left.mid.cortex_smooth10_smooth10.dfs
Error in surf_align_autocorrect_with_AIR (line 159)
Error in align_surf_curves (line 62)
Error in surf_flatten_newbs (line 32)
Error in svreg_label_surf_hemi (line 163)
another is the pial line. While brainsuite is running, i can see that it was too much inside the brain, sometimes including the inner temporal!!!