#!/bin/bash
#SBATCH --job-name reg_MTL0002
#SBATCH --time=08:00:00
#SBATCH -n 1
#SBATCH --account=def-villens
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G
#SBATCH --mail-type=None


ml VilleneuveLab
ml StdEnv/2020
ml gcc/9.3.0
ml ants

tedana_native=/lustre04/scratch/javan/ME_Feb2024/wave2_final/derivatives/tedana/sub-MTL0002_ses-FU84/sub-MTL0002_ses-FU84_task-_space-Native_desc-optcomDenoised_bold.nii.gz

tedana_MNI=/lustre04/scratch/javan/ME_Feb2024/wave2_final/registration/derivatives_reg/sub-MTL0002/sub-MTL0002_ses-FU84_task-_space-MNI152NLin2009cAsym_desc-optcomDenoised_bold.nii.gz

boldref2T1w=/lustre04/scratch/javan/ME_Feb2024/wave2_final/derivatives/sub-MTL0002/sub-MTL0002/ses-FU84/func/sub-MTL0002_ses-FU84_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt

T1w2MNI=/lustre04/scratch/javan/ME_Feb2024/wave2_final/derivatives/sub-MTL0002/sub-MTL0002/ses-FU84/anat/sub-MTL0002_ses-FU84_acq-MPRAGE_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5

reference=/lustre04/scratch/javan/ME_Feb2024/wave2_final/derivatives/sub-MTL0002/sub-MTL0002/ses-FU84/func/sub-MTL0002_ses-FU84_task-rest_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz

antsApplyTransforms --dimensionality 3 \
 --input-image-type 3 \
 --input ${tedana_native} \
 --reference-image ${reference} \
 --output ${tedana_MNI} \
 --interpolation LanczosWindowedSinc \
 --transform ${boldref2T1w} \
 --transform ${T1w2MNI} \
 --default-value 0 \
 --float 1 \
 --verbose 1