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Stereo spm #234

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merged 6 commits into from
Nov 23, 2023
Merged

Stereo spm #234

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9665c33
adding stereo to spm_native pipeline
davidmeunier79 Nov 23, 2023
e75ad6d
typo
davidmeunier79 Nov 23, 2023
0fbfc4f
doublon
davidmeunier79 Nov 23, 2023
94902f4
rename stereo spm
davidmeunier79 Nov 23, 2023
0056ff7
flake8
davidmeunier79 Nov 23, 2023
2977324
params_template_stereo in spm pipeline
davidmeunier79 Nov 23, 2023
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104 changes: 103 additions & 1 deletion macapype/pipelines/full_pipelines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@

def create_full_spm_subpipes(
params_template, params_template_aladin,
params_template_stereo,
params={}, name='full_spm_subpipes',
pad=False, space='template'):
""" Description: SPM based segmentation pipeline from T1w and T2w images
Expand Down Expand Up @@ -130,7 +131,11 @@ def create_full_spm_subpipes(
niu.IdentityInterface(fields=['brain_mask', 'segmented_brain_mask',
'debiased_T1', 'debiased_brain',
"wmgm_stl",
'prob_wm', 'prob_gm', 'prob_csf']),
'prob_wm', 'prob_gm', 'prob_csf',
'stereo_native_T1', 'stereo_debiased_T1',
'stereo_brain_mask',
'stereo_segmented_brain_mask',
"native_to_stereo_trans"]),
name='outputnode')
# preprocessing
if 'long_single_preparation_pipe' in params.keys():
Expand Down Expand Up @@ -234,6 +239,27 @@ def create_full_spm_subpipes(
seg_pipe.connect(pad_debiased_T1, "padded_img_file",
outputnode, "debiased_T1")

print("Padding debiased_T2 in native space")
pad_debiased_T2 = pe.Node(
niu.Function(
input_names=['cropped_img_file', 'orig_img_file',
'indiv_crop'],
output_names=['padded_img_file'],
function=padding_cropped_img),
name="pad_debiased_T2")

seg_pipe.connect(debias, 't2_debiased_file',
pad_debiased_T2, "cropped_img_file")

seg_pipe.connect(data_preparation_pipe, "outputnode.native_T2",
pad_debiased_T2, "orig_img_file")

seg_pipe.connect(inputnode, "indiv_params",
pad_debiased_T2, "indiv_crop")

seg_pipe.connect(pad_debiased_T2, "padded_img_file",
outputnode, "debiased_T2")

print("Padding debiased_brain in native space")
pad_debiased_brain = pe.Node(
niu.Function(
Expand Down Expand Up @@ -381,6 +407,64 @@ def create_full_spm_subpipes(
seg_pipe.connect(debias, 't1_debiased_file',
outputnode, "debiased_T1")

if "native_to_stereo_pipe" in params.keys():

native_to_stereo_pipe = create_native_to_stereo_pipe(
"native_to_stereo_pipe",
params=parse_key(params, "native_to_stereo_pipe"))

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.native_to_stereo_trans',
outputnode, 'native_to_stereo_trans')

# full head version
seg_pipe.connect(data_preparation_pipe, "outputnode.native_T1",
native_to_stereo_pipe, 'inputnode.native_T1')

native_to_stereo_pipe.inputs.inputnode.stereo_T1 = \
params_template_stereo["template_head"]

seg_pipe.connect(native_to_stereo_pipe,
"outputnode.stereo_native_T1",
outputnode, "stereo_native_T1")

if pad:

# apply transfo to list
apply_stereo_mask = pe.Node(RegResample(inter_val="NN"),
name='apply_stereo_mask')

seg_pipe.connect(pad_mask, 'out_file',
apply_stereo_mask, "flo_file")
seg_pipe.connect(native_to_stereo_pipe,
'outputnode.native_to_stereo_trans',
apply_stereo_mask, "trans_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.padded_stereo_T1',
apply_stereo_mask, "ref_file")

seg_pipe.connect(apply_stereo_mask, "out_file",
outputnode, "stereo_brain_mask")

# apply transfo to list
apply_stereo_debiased_T1 = pe.Node(RegResample(),
name='apply_stereo_debiased_T1')

seg_pipe.connect(pad_debiased_T1, 'out_file',
apply_stereo_debiased_T1, "flo_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.native_to_stereo_trans',
apply_stereo_debiased_T1, "trans_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.padded_stereo_T1',
apply_stereo_debiased_T1, "ref_file")

seg_pipe.connect(apply_stereo_debiased_T1, "out_file",
outputnode, "stereo_debiased_T1")

# Iterative registration to the INIA19 template
reg = NodeParams(IterREGBET(),
params=parse_key(params, "reg"),
Expand Down Expand Up @@ -755,11 +839,29 @@ def create_full_spm_subpipes(
seg_pipe.connect(pad_seg_mask, "padded_img_file",
outputnode, "segmented_brain_mask")

if "native_to_stereo_pipe" in params:

# apply transfo to seg_mask
apply_stereo_seg_mask = pe.Node(RegResample(inter_val="NN"),
name='apply_stereo_seg_mask')

seg_pipe.connect(pad_seg_mask, 'out_file',
apply_stereo_seg_mask, "flo_file")
seg_pipe.connect(native_to_stereo_pipe,
'outputnode.native_to_stereo_trans',
apply_stereo_seg_mask, "trans_file")
seg_pipe.connect(native_to_stereo_pipe,
'outputnode.padded_stereo_T1',
apply_stereo_seg_mask, "ref_file")

seg_pipe.connect(apply_stereo_seg_mask, "out_file",
outputnode, "stereo_segmented_brain_mask")
else:
seg_pipe.connect(mask_from_seg_pipe,
'merge_indexed_mask.indexed_mask',
outputnode, 'segmented_brain_mask')

# LEGACY
if space == 'template':

# not mandatory
Expand Down
119 changes: 87 additions & 32 deletions macapype/pipelines/rename.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -315,6 +315,42 @@ def rename_all_derivatives(params, main_workflow, segment_pnh_pipe,
rename_prob_csf, 'out_file',
datasink, '@prob_csf')

if "mask_from_seg_pipe" in params.keys():

# rename segmented_brain_mask
rename_segmented_brain_mask = pe.Node(
niu.Rename(),
name="rename_segmented_brain_mask")
rename_segmented_brain_mask.inputs.format_string = \
pref_deriv + "_space-{}_desc-brain_dseg".format(space)
rename_segmented_brain_mask.inputs.parse_string = parse_str
rename_segmented_brain_mask.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.segmented_brain_mask',
rename_segmented_brain_mask, 'in_file')

main_workflow.connect(
rename_segmented_brain_mask, 'out_file',
datasink, '@segmented_brain_mask')

print("Renaming wmgm_stl file")

rename_wmgm_stl = pe.Node(niu.Rename(),
name="rename_wmgm_stl")
rename_wmgm_stl.inputs.format_string = \
pref_deriv + "_space-{}_desc-wmgm_mask".format(space)
rename_wmgm_stl.inputs.parse_string = parse_str
rename_wmgm_stl.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.wmgm_stl',
rename_wmgm_stl, 'in_file')

main_workflow.connect(
rename_wmgm_stl, 'out_file',
datasink, '@wmgm_stl')

if "native_to_stereo_pipe" in params.keys():

# rename stereo_native_T1
Expand Down Expand Up @@ -368,6 +404,41 @@ def rename_all_derivatives(params, main_workflow, segment_pnh_pipe,
rename_stereo_debiased_T1, 'out_file',
datasink, '@stereo_debiased_T1')

elif "debias" in params.keys():
# rename stereo_brain_mask
rename_stereo_brain_mask = pe.Node(
niu.Rename(),
name="rename_stereo_brain_mask")
rename_stereo_brain_mask.inputs.format_string = \
pref_deriv + "_space-stereo_desc-brain_mask"
rename_stereo_brain_mask.inputs.parse_string = parse_str
rename_stereo_brain_mask.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.stereo_brain_mask',
rename_stereo_brain_mask, 'in_file')

main_workflow.connect(
rename_stereo_brain_mask, 'out_file',
datasink, '@stereo_brain_mask')

# rename stereo_debiased_T1
rename_stereo_debiased_T1 = pe.Node(
niu.Rename(),
name="rename_stereo_debiased_T1")
rename_stereo_debiased_T1.inputs.format_string = \
pref_deriv + "_space-stereo_desc-debiased_T1w"
rename_stereo_debiased_T1.inputs.parse_string = parse_str
rename_stereo_debiased_T1.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.stereo_debiased_T1',
rename_stereo_debiased_T1, 'in_file')

main_workflow.connect(
rename_stereo_debiased_T1, 'out_file',
datasink, '@stereo_debiased_T1')

if "brain_segment_pipe" in params.keys():

# rename stereo_segmented_brain_mask
Expand Down Expand Up @@ -440,38 +511,22 @@ def rename_all_derivatives(params, main_workflow, segment_pnh_pipe,
rename_stereo_prob_csf, 'out_file',
datasink, '@stereo_prob_csf')

if "mask_from_seg_pipe" in params.keys():

# rename segmented_brain_mask
rename_segmented_brain_mask = pe.Node(
niu.Rename(),
name="rename_segmented_brain_mask")
rename_segmented_brain_mask.inputs.format_string = \
pref_deriv + "_space-{}_desc-brain_dseg".format(space)
rename_segmented_brain_mask.inputs.parse_string = parse_str
rename_segmented_brain_mask.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.segmented_brain_mask',
rename_segmented_brain_mask, 'in_file')

main_workflow.connect(
rename_segmented_brain_mask, 'out_file',
datasink, '@segmented_brain_mask')

print("Renaming wmgm_stl file")
elif "mask_from_seg_pipe" in params:
# rename stereo_segmented_brain_mask
rename_stereo_segmented_brain_mask = pe.Node(
niu.Rename(),
name="rename_stereo_segmented_brain_mask")

rename_wmgm_stl = pe.Node(niu.Rename(),
name="rename_wmgm_stl")
rename_wmgm_stl.inputs.format_string = \
pref_deriv + "_space-{}_desc-wmgm_mask".format(space)
rename_wmgm_stl.inputs.parse_string = parse_str
rename_wmgm_stl.inputs.keep_ext = True
rename_stereo_segmented_brain_mask.inputs.format_string =\
pref_deriv + "_space-stereo_desc-brain_dseg"
rename_stereo_segmented_brain_mask.inputs.parse_string = \
parse_str
rename_stereo_segmented_brain_mask.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.wmgm_stl',
rename_wmgm_stl, 'in_file')
main_workflow.connect(
segment_pnh_pipe, 'outputnode.stereo_segmented_brain_mask',
rename_stereo_segmented_brain_mask, 'in_file')

main_workflow.connect(
rename_wmgm_stl, 'out_file',
datasink, '@wmgm_stl')
main_workflow.connect(
rename_stereo_segmented_brain_mask, 'out_file',
datasink, '@stereo_segmented_brain_mask')
3 changes: 2 additions & 1 deletion macapype/pipelines/tests/test_full_pipelines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,8 @@ def test_create_full_spm_subpipes_all_default_params():
# running workflow
segment_pnh = create_full_spm_subpipes(
params=params, params_template=params_template,
params_template_aladin=params_template, space=space,
params_template_aladin=params_template,
params_template_stereo=params_template, space=space,
name="test_create_full_ants_subpipes_all_default_params")

segment_pnh.base_dir = data_path
Expand Down
16 changes: 16 additions & 0 deletions workflows/params_segment_macaque_spm.json
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,22 @@
"kernel_size": 2
}
},
"native_to_stereo_pipe":
{
"pad_template_T1":
{
"pad_val": 20
},
"reg_T1_on_template":
{
"nac_flag": true,
"rig_only_flag":true,
"nosym_flag": true,
"ln_val" : 12,
"lp_val": 10,
"smoo_r_val" : 1.0
}
},
"regex_subs":
{
"FLAIR_flirt": "preproc-coreg_FLAIR"
Expand Down
1 change: 1 addition & 0 deletions workflows/segment_pnh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -367,6 +367,7 @@ def create_main_workflow(data_dir, process_dir, soft, species, subjects,
segment_pnh_pipe = create_full_spm_subpipes(
params_template=params_template,
params_template_aladin=params_template_aladin,
params_template_stereo=params_template_stereo,
params=params, pad=pad, space=space)

elif "ants" in ssoft:
Expand Down
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