Added intersectional template masking and different clamping for last iteration

test.sh

-#!/bin/bash 
-#SBATCH --partition=long 
-#SBATCH -o /data/users/u7pt4u/out.out 
-#SBATCH -e /data/users/u7pt4u/error.err
-#SBATCH --time=05:00
-
-applywarp -i /data/ms/processed/mri/Jacobian/fsl/sub-CFTY720D2301x0101x00002/ses-V9x20070615/anat/T1Gd_biascorr_normalised_nogm.nii.gz -o /data/users/u7pt4u/test_output.nii.gz -r /data/ms/processed/mri/Jacobian/fsl/median_hybrid/CFTY720D2301/sub-CFTY720D2301x0101x00002/SST_FSL/nln_step_05/iteration_01/nln_template_T1_head_05_01.nii.gz -w /data/ms/processed/mri/Jacobian/fsl/median_hybrid/CFTY720D2301/sub-CFTY720D2301x0101x00002/SST_FSL/nln_step_06/iteration_01/ses-V9x20070615_to_template_warp_resampled_unbiased_full_T1_head.nii.gz --interp=spline
\ No newline at end of file

test1.sh

-#!/bin/bash
-#SBATCH --partition=long
-#SBATCH -o /data/users/u7pt4u/out.out
-#SBATCH -e /data/users/u7pt4u/error.err
-#SBATCH --time=05:00
-
-python /data/users/u7pt4u/ms-templates/code/test2.py
\ No newline at end of file

test2.py

-from fsl.wrappers.fnirt import invwarp, applywarp, convertwarp
-import nibabel as nib
-img_nib = nib.load('/data/ms/processed/mri/Jacobian/fsl/sub-CFTY720D2301x0101x00002/ses-V9x20070615/anat/T1_biascorr_normalised_nogm.nii.gz')
-applywarp(src=img_nib, ref="/data/users/u7pt4u/ms-templates/data/processed/sub-CFTY720D2301x0101x00002/nln_step_06/iteration_01/nln_template_T1_head_06_01.nii.gz", out="/data/users/u7pt4u/ms-templates/data/processed/sub-CFTY720D2301x0101x00002/test_output_fslpy_submit_node.nii.gz", warp="/data/users/u7pt4u/ms-templates/data/processed/sub-CFTY720D2301x0101x00002/nln_step_07/iteration_01/ses-V9x20070615_to_template_warp_resampled_unbiased_full_T1_head.nii.gz", interp="spline")
-