Commit 5532b5c6 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

inverse mask creation, intensity normalisation=False, delete all temporary files when clamping

parent 4d65e120
......@@ -852,6 +852,7 @@ if __name__ == "__main__":
kwargs=None,
clean="never")
jobcmd = jobcmd + '\n'
jobcmd = jobcmd + 'fslmaths ' + tree.get('data/lesion_mask_in_T1') + ' -bin ' + tree.get('inverse_lesion_mask_in_T1') + '\n'
f.write(jobcmd)
# job_ids[0] = submitJob(tag+'_'+task_name, log_dir, script=script_path, queue=cpuq)
job_ids[0] = submitJob(script_path, tag+'_'+task_name, log_dir, queue=cpuq, wait_for=None, array_task=True)
......@@ -996,7 +997,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('T1_to_unbiased_img'))
aff_template_path = tree.get('T1_unbiased_affine_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', True), tmp_dir=script_dir, kwargs=None,
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', False), tmp_dir=script_dir, kwargs=None,
clean="never")
# job_ids[8] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[5]])
job_ids[8] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[5]],
......@@ -1188,7 +1189,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('T1_brain_to_MNI_img'))
aff_template_path = tree.get('T1_brain_affine_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[21] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[15]])
......@@ -1231,7 +1232,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('T1_head_to_MNI_img'))
aff_template_path = tree.get('T1_head_affine_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[24] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[17]])
......@@ -1249,7 +1250,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('T2_head_to_MNI_img'))
aff_template_path = tree.get('T2_head_affine_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[25] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[18]])
......@@ -1267,7 +1268,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('DTI_to_MNI_img'))
aff_template_path = tree.get('DTI_affine_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, aff_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[26] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[19]])
......@@ -1377,7 +1378,7 @@ if __name__ == "__main__":
aff_ref_scalar = [tree.get('identity_mat')]
aff_mov_scalar = [tree.get('T1_to_MNI_mat')]
mask_ref_scalar = [img_ref_T1brain_mask_path]
mask_mov_scalar = [tree.get('data/lesion_mask_in_T1')]
mask_mov_scalar = [tree.get('data/inverse_lesion_mask_in_T1')]
img_ref_tensor = []
img_mov_tensor = []
aff_ref_tensor = []
......@@ -1710,7 +1711,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('warped_T1brain'))
nln_template_path = tree.get('T1_brain_nln_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[44] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[37]])
......@@ -1728,7 +1729,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('warped_T1head'))
nln_template_path = tree.get('T1_head_nln_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[45] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[39]])
......@@ -1746,7 +1747,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('warped_T2head'))
nln_template_path = tree.get('T2_head_nln_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[46] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[40]])
......@@ -1764,7 +1765,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('warped_DTIscalar'))
nln_template_path = tree.get('DTI_nln_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', True), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'median', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[47] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq,
# wait_for=[job_ids[42]])
......
......@@ -8,11 +8,11 @@ ext_txt=.txt
!{template_dir}
misc (misc_dir)
ident{ext_mat} (identity_mat)
log (log_dir)
scripts (script_dir)
clamped_T1 (clamped_dir)
{sub_id}
{sub_id}_T1_clamped{ext_nii} (T1_head_clamped)
{sub_id}_T2Lesion_in_T1_inverse{ext_nii} (inverse_lesion_mask_in_T1)
log (log_dir)
scripts (script_dir)
affine_it1 (affine_it1_dir)
{sub_id} (affine_it1_subject_dir)
T1_to_{ref_id}{ext_mat} (T1_to_ref_mat)
......
......@@ -6,4 +6,4 @@ ext_mat=.mat
T1_orig{ext_nii} (T1_head)
T1_brain{ext_nii} (T1_brain)
T1_brain_mask{ext_nii} (T1_brain_mask)
T2Lesion_in_T1{ext_nii} (lesion_mask_in_T1)
\ No newline at end of file
T2Lesion_in_T1{ext_nii} (lesion_mask_in_T1)
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