setenv SUBJECTS_DIR /autofs/cluster/transcend/MRI/WMA/recons
set dtroot = /autofs/space/glia_001/users/shantanu/dtistudy
set subjlist = ( 007501)
set dcmroot = /autofs/cluster/transcend/MRI/WMA/DICOM
 
set dcmlist = ( 005801/108000-000014-000001.dcm \
                007501/823000-000012-000001.dcm  )
set bvecfile = /autofs/cluster/transcend/MRI/WMA/dti/008801/bvecs
set bvalfile = /autofs/cluster/transcend/MRI/WMA/dti/008801/bvals
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
set cvstemp = cvs_avg35
set cvstempdir = $FREESURFER_HOME/subjects
set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.ilf_AS rh.ilf_AS \
                 lh.unc_AS rh.unc_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
set nstick = 2
set nburnin = 200
set nsample = 7500
set nkeep = 5
set reinit = 0