# Run command file generated automatically by trac-all
#
setenv FREESURFER_HOME /Applications/freesurfer/7.3.2
setenv SUBJECTS_DIR /Users/corpuscallosum/Desktop/Freesurfer/BRASS
set dtroot = (/Users/corpuscallosum/Desktop/Freesurfer/BRASS/R001A)
set subj = (R001A)
#
# Processing steps to be performed
#
set docorr = (1)
set doqa = (1)
set dointra = (1)
set dotensor = (1)
set dointer = (1)
set dopriors = (1)
#
# Options for image corrections and tensor fit
#
set dcmroot = (/Users/corpuscallosum/Desktop/Freesurfer/BRASS/R001A/R001A.dicom)
set dcmfile = (1.2.840.113619.2.475.14196467.3448649.2049.1682210291.210.MR.dcm)
set bvecfile = ()
set bvalfile = ()
set bmax = ()
set bshell = ()
set nb0 = ()
set dob0 = (0)
set b0mfile = ()
set b0pfile = ()
set echospacing = (0.7)
set epifactor = (65)
set pedir = (RL)
set dTE = ()
set doeddy = (0)
set dorotbvecs = (1)
set thrbet = (0.3)
#
# Options for registrations
#
set intrareg = (3)
set intracost = ()
set intradof = (9)
set intrarot = (90)
set interreg = (5)
set intercost = ()
set intertrg = (/Applications/freesurfer/7.3.2/trctrain/hcp/MGH35_HCP_FA_template.nii.gz)
#
# Options for anatomical segmentation
#
set segname = (aparc+aseg)
set gmgrow = (2)
set usethalnuc = (0)
set usemaskanat = (1)
#
# Options for ball-and-stick model fit
#
set nstick = (2)
#
# Options for path reconstructions
#
set pathlist = (acomm cc.bodyc cc.bodyp cc.bodypf cc.bodypm cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af rh.af lh.ar rh.ar lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf)
set gmids = (0 0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0)
set ncpts = (7 8 9 7 7 12 5 5 7 7 9 9 4 4 4 4 7 7 5 5 7 7 7 7 5 5 9 9 8 8 7 7 5 5 7 7 8 8 6 6 7 7)
set trainsubjlist = ($FREESURFER_HOME/trctrain/hcp/mgh_1001 $FREESURFER_HOME/trctrain/hcp/mgh_1006 $FREESURFER_HOME/trctrain/hcp/mgh_1007 $FREESURFER_HOME/trctrain/hcp/mgh_1008 $FREESURFER_HOME/trctrain/hcp/mgh_1009 $FREESURFER_HOME/trctrain/hcp/mgh_1010 $FREESURFER_HOME/trctrain/hcp/mgh_1011 $FREESURFER_HOME/trctrain/hcp/mgh_1012 $FREESURFER_HOME/trctrain/hcp/mgh_1013 $FREESURFER_HOME/trctrain/hcp/mgh_1015 $FREESURFER_HOME/trctrain/hcp/mgh_1016 $FREESURFER_HOME/trctrain/hcp/mgh_1017 $FREESURFER_HOME/trctrain/hcp/mgh_1019 $FREESURFER_HOME/trctrain/hcp/mgh_1021 $FREESURFER_HOME/trctrain/hcp/mgh_1023 $FREESURFER_HOME/trctrain/hcp/mgh_1024)
set ntrainlist = (16)
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 pmin = (.2)
set projmin = (-3)
set projmax = (3)
set dproj = (.1)
set overwrite = (1)
#
# Location of TRACULA executables
#
set trcdir = (/Applications/freesurfer/7.3.2/bin)