#see: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula/
#
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#

setenv SUBJECTS_DIR /project/3015068.01/ilecam/RUNDMC_dwi_2015/subset_declined_constant/test_tracula/freesurfer


# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
## change this
set dtroot = /project/3015068.01/ilecam/RUNDMC_dwi_2015/subset_declined_constant/test_tracula/freesurfer/tracula_out/sub025

# Subject IDs
# (pretend something is a subject id for tracula - it is just the next level down from the SUBJECTS_DIR above)
set subjlist = ( sub025 )

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified
#
set dcmroot = /project/3015068.01/ilecam/RUNDMC_dwi_2015/subset_declined_constant/test_tracula/sub025/FDT_Data

# motion & eddy corrected, clean diffusion data and bvecs and bvals (only the latter two require full path)
set dcmlist = ( data.nii )		# deleted gz
set bvecfile = ( $dcmroot/bvecs )
set bvalfile = ( $dcmroot/bvals )

set dorotbvecs = 0 # set to 0 if the results is the same as my rotated bvecs

set usemaskanat = 1 #uses Freesurfer seg and avoids setting variable bet thresholds as used in FDT
#set thrbet = 0.2 # previous value for bet????? #not necessary if above = 1

set doregflt = 0 #do flirt instead of bbregister?
set doregbbr = 1
### because marcel's preproc is better than eddy_correct
set dob0 = 0
set doeddy = 0

set doregmni = 1
set doregcvs = 0

#set pathlist = ( fmajor_PP )  #### TO TEST
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 ) 
#add/remove tracts if desired

#set ncpts = ( 7 ) #adjust/add points to match pathlist
set ncpts = ( 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 )

set nb0 = 7 #number of b0 images