#!/bin/tcsh
set workingDIR = "/data/blt/TRACULA"
set SUBJECTS_DIR = $workingDIR/diffusion_recons
setenv SUBJECTS_DIR $workingDIR/diffusion_recons
set dtroot =  $workingDIR/tractography_output

set subjlist = ( BL01_1 \
BL28_1 \
BL28_2 \
BL29_1 \
BL29_2 \
BL31_1 \
BL31_2 \
BL32_1 \
BL32_2 \
BL33_1 \
BL33_2 \
BL34_1 \
BL34_2 )

set baselist= ( BL01_1 \
BL01_2 \
BL02_1 \
BL02_2 \
BL04_1 \
BL04_2 \
BL05_1 \
BL05_2 \
BL06_1 \
BL06_2 \
BL07_1 \
BL07_2 \
BL08_1 \
BL08_2 \
BL10_1 \
BL10_2 \
BL11_1 \
BL11_2 \
BL12_1 \
BL12_2 \
BL13_1 \
BL13_2 \
BL14_1 \
BL14_2 \
BL15_1 \
BL15_2 \
BL16_1 \
BL16_2 \
BL19_1 \
BL19_2 \
BL23_1 \
BL23_2 \
BL24_1 \
BL24_2 \
BL25_1 \
BL25_2 \
BL26_1 \
BL26_2 \
BL27_1 \
BL27_2 \
BL28_1 \
BL28_2 \
BL29_1 \
BL29_2 \
BL31_1 \
BL31_2 \
BL32_1 \
BL32_2 \
BL33_1 \
BL33_2 \
BL34_1 \
BL34_2 )

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

set doregmni = 1

set doregcvs = 0

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)