#!/bin/bash

rapidtide \
    --spatialfilt 2 \
    --nprocs -1 \
    --passes 3 \
    --simcalcrange 50 -1 \
    sub-RAPIDTIDETEST.nii.gz \
    ../dst/sub-RAPIDTIDETEST_nomask

rapidtide \
    --spatialfilt 2 \
    --nprocs -1 \
    --passes 3 \
    --simcalcrange 50 -1 \
    --brainmask sub-RAPIDTIDETEST_restrictedmask.nii.gz \
    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
    sub-RAPIDTIDETEST.nii.gz \
    ../dst/sub-RAPIDTIDETEST_masks

#for FILT in 1 2 4 8 16
#do
#    rapidtide \
#        --spatialfilt ${FILT} \
#        --nprocs -1 \
#        --passes 3 \
#        --simcalcrange 50 -1 \
#        --outputlevel min \
#        sub-RAPIDTIDETEST.nii.gz \
#        ../dst/sub-RAPIDTIDETEST_${FILT}
#done
#
#for MAP in maxtime maxcorr
#do
#    fslmerge -t ../dst/all_${MAP} \
#        ../dst/sub-RAPIDTIDETEST_1_desc-${MAP}_map.nii.gz \
#        ../dst/sub-RAPIDTIDETEST_2_desc-${MAP}_map.nii.gz \
#        ../dst/sub-RAPIDTIDETEST_4_desc-${MAP}_map.nii.gz \
#        ../dst/sub-RAPIDTIDETEST_8_desc-${MAP}_map.nii.gz \
#        ../dst/sub-RAPIDTIDETEST_16_desc-${MAP}_map.nii.gz 
#done
