#!/bin/tcsh

# SSW: run @SSwarper to skullstrip (SS) and estimate a nonlinear warp.

# Process a single subj+ses pair.  Run this script in
# apmulti_demo/scripts/, via the corresponding run_*tcsh script.

# ---------------------------------------------------------------------------
# top level definitions (constant across demo)
# ---------------------------------------------------------------------------
 
# labels
set subj           = $1
set ses            = $2

set template       = MNI152_2009_template_SSW.nii.gz 

# upper directories
set dir_inroot     = ${PWD:h}                        # one dir above scripts/
set dir_log        = ${dir_inroot}/logs
set dir_basic      = ${dir_inroot}/data_00_basic
set dir_fs         = ${dir_inroot}/data_12_fs
set dir_ssw        = ${dir_inroot}/data_13_ssw

# subject directories
set sdir_basic     = ${dir_basic}/${subj}/${ses}
set sdir_epi       = ${sdir_basic}/func
set sdir_fs        = ${dir_fs}/${subj}/${ses}
set sdir_suma      = ${sdir_fs}/SUMA
set sdir_ssw       = ${dir_ssw}/${subj}/${ses}

# --------------------------------------------------------------------------
# data and control variables
# --------------------------------------------------------------------------

# dataset inputs
set dset_anat_00  = ${sdir_basic}/anat/${subj}_${ses}_mprage_run-1_T1w.nii.gz

# control variables

# check available N_threads and report what is being used
# + consider using up to 16 threads (alignment programs are parallelized)
# + N_threads may be set elsewhere; to set here, uncomment the following line:
### setenv OMP_NUM_THREADS 16

set nthr_avail = `afni_system_check.py -disp_num_cpu`
set nthr_using = `afni_check_omp`

echo "++ INFO: Using ${nthr_avail} of available ${nthr_using} threads"

# ---------------------------------------------------------------------------
# run programs
# ---------------------------------------------------------------------------

time @SSwarper                                                        \
    -base    "${template}"                                            \
    -subid   "${subj}"                                                \
    -input   "${dset_anat_00}"                                        \
    -odir    "${sdir_ssw}"

echo "++ FINISHED SSW"

exit 0