# Run command file generated automatically by trac-all
#
# This is a time point for longitudinal tractography
#
setenv FREESURFER_HOME /usr/local/packages/freesurfer-v5.3.0
setenv SUBJECTS_DIR /data/napls_DTI/TSS/fs_tracula/fsrecon
set dtroot = (/mnt/nfs/napls_DTI/TSS/fs_tracula/DTI)
set subj = (01_V1000_2_01)
#
# Processing steps to be performed
#
set docorr = (1)
set dointra = (1)
set dointer = (1)
set domasks = (1)
set dotensor = (1)
set dopriors = (0)
#
# Options for image corrections and tensor fit
#
set dcmroot = (/mnt/nfs/napls_DTI/TSS/fs_tracula/DTI)
set dcmfile = (01_V1000_2_01/DTI_31_dir.nii)
set bvecfile = (/mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/bvec.txt)
set bvalfile = (/mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/bval.txt)
set nb0 = ()
set dob0 = (0)
set b0mfile = ()
set b0pfile = ()
set echospacing = ()
set doeddy = (1)
set dorotbvecs = (1)
set thrbet = (0.3)
set usemaskanat = (1)
#
# Options for registrations
#
set doregflt = (0)
set doregbbr = (1)
set doregmni = (1)
set doregcvs = (0)
set mnitemp = (/usr/local/packages/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz)
set cvstempdir = (/usr/local/packages/freesurfer/subjects)
set cvstemp = (cvs_avg35)
#
# Options for ball-and-stick model fit
#
set nstick = (2)
#
# Options for path reconstructions
#
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.ccg_PP rh.ccg_PP lh.cab_PP rh.cab_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 trainsubjlist = ($FREESURFER_HOME/trctrain/trc001 $FREESURFER_HOME/trctrain/trc002 $FREESURFER_HOME/trctrain/trc003 $FREESURFER_HOME/trctrain/trc004 $FREESURFER_HOME/trctrain/trc005 $FREESURFER_HOME/trctrain/trc006 $FREESURFER_HOME/trctrain/trc007 $FREESURFER_HOME/trctrain/trc008 $FREESURFER_HOME/trctrain/trc009 $FREESURFER_HOME/trctrain/trc010 $FREESURFER_HOME/trctrain/trc011 $FREESURFER_HOME/trctrain/trc012 $FREESURFER_HOME/trctrain/trc013 $FREESURFER_HOME/trctrain/trc014 $FREESURFER_HOME/trctrain/trc015 $FREESURFER_HOME/trctrain/trc016 $FREESURFER_HOME/trctrain/trc017 $FREESURFER_HOME/trctrain/trc018 $FREESURFER_HOME/trctrain/trc019 $FREESURFER_HOME/trctrain/trc020 $FREESURFER_HOME/trctrain/trc021 $FREESURFER_HOME/trctrain/trc022 $FREESURFER_HOME/trctrain/trc023 $FREESURFER_HOME/trctrain/trc024 $FREESURFER_HOME/trctrain/trc025 $FREESURFER_HOME/trctrain/trc026 $FREESURFER_HOME/trctrain/trc027 $FREESURFER_HOME/trctrain/trc028 $FREESURFER_HOME/trctrain/trc029 $FREESURFER_HOME/trctrain/trc030 $FREESURFER_HOME/trctrain/trc031 $FREESURFER_HOME/trctrain/trc032 $FREESURFER_HOME/trctrain/trc033)
set ntrainlist = (33)
set avgname = (avg)
set reinit = (0)
set usetrunc = (1)
set doxyzprior = (0)
set dosegprior = (1)
set dotangprior = (0)
set dopathsubdirs = (0)
set fmin = (0.05)
set nburnin = (200)
set nsample = (7500)
set nupdate = (0)
set nkeep = (5)
set doinitprop = (1)
set overwrite = (1)
#
# Location of TRACULA executables
#
set trcdir = (/usr/local/packages/freesurfer/bin)