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@davidmeunier79
davidmeunier79 committed Dec 21, 2023
1 parent 48c0b67 commit 54da897
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Showing 4 changed files with 79 additions and 75 deletions.
108 changes: 57 additions & 51 deletions macapype/pipelines/full_pipelines.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -548,63 +548,65 @@ def create_full_spm_subpipes(
'inputnode.native_T1')

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.stereo_native_T1',
outputnode, "stereo_debiased_T2")
'outputnode.stereo_native_T1',
outputnode, "stereo_debiased_T2")

# apply stereo to debiased T1
apply_stereo_debiased_T1 = pe.Node(RegResample(pad_val=0.0),
name='apply_stereo_debiased_T1')
apply_stereo_debiased_T1 = pe.Node(
RegResample(pad_val=0.0),
name='apply_stereo_debiased_T1')

seg_pipe.connect(pad_masked_debiased_T1, "out_file",
apply_stereo_debiased_T1, "flo_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")
'outputnode.native_to_stereo_trans',
apply_stereo_debiased_T1, "trans_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.stereo_native_T1',
apply_stereo_debiased_T1, "ref_file")
'outputnode.stereo_native_T1',
apply_stereo_debiased_T1, "ref_file")

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

outputnode, "stereo_debiased_T1")

else:
seg_pipe.connect(pad_masked_debiased_T1, "out_file",
native_to_stereo_pipe,
'inputnode.native_T1')

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.stereo_native_T1',
outputnode, "stereo_debiased_T1")
'outputnode.stereo_native_T1',
outputnode, "stereo_debiased_T1")

# apply stereo to debiased T2
apply_stereo_debiased_T2 = pe.Node(RegResample(pad_val=0.0),
name='apply_stereo_debiased_T2')
apply_stereo_debiased_T2 = pe.Node(
RegResample(pad_val=0.0),
name='apply_stereo_debiased_T2')

seg_pipe.connect(pad_masked_debiased_T2, "out_file",
apply_stereo_debiased_T2, "flo_file")
apply_stereo_debiased_T2, "flo_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.native_to_stereo_trans',
apply_stereo_debiased_T2, "trans_file")
'outputnode.native_to_stereo_trans',
apply_stereo_debiased_T2, "trans_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.stereo_debiased_T2',
apply_stereo_debiased_T2, "ref_file")
'outputnode.stereo_debiased_T2',
apply_stereo_debiased_T2, "ref_file")

# output
seg_pipe.connect(apply_stereo_debiased_T2, "out_file",
outputnode, "stereo_debiased_T2")
outputnode, "stereo_debiased_T2")

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

# apply stereo to native T1
apply_stereo_native_T1 = pe.Node(RegResample(pad_val = 0.0),
name='apply_stereo_native_T1')
apply_stereo_native_T1 = pe.Node(
RegResample(pad_val=0.0),
name='apply_stereo_native_T1')

seg_pipe.connect(data_preparation_pipe, "outputnode.native_T1",
apply_stereo_native_T1, "flo_file")
Expand Down Expand Up @@ -643,17 +645,18 @@ def create_full_spm_subpipes(
name='apply_stereo_mask')

seg_pipe.connect(pad_mask, 'out_file',
apply_stereo_mask, "flo_file")
apply_stereo_mask, "flo_file")

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

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

else:
# full head version
Expand Down Expand Up @@ -682,40 +685,42 @@ def create_full_spm_subpipes(
if pad:

# apply stereo to debiased T1
apply_stereo_debiased_T1 = pe.Node(RegResample(pad_val=0.0),
name='apply_stereo_debiased_T1')
apply_stereo_debiased_T1 = pe.Node(
RegResample(pad_val=0.0),
name='apply_stereo_debiased_T1')

seg_pipe.connect(pad_masked_debiased_T1, "out_file",
apply_stereo_debiased_T1, "flo_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")
'outputnode.native_to_stereo_trans',
apply_stereo_debiased_T1, "trans_file")

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.stereo_native_T1',
apply_stereo_debiased_T1, "ref_file")
'outputnode.stereo_native_T1',
apply_stereo_debiased_T1, "ref_file")

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

# 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")
apply_stereo_mask, "flo_file")

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

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

# Iterative registration to the INIA19 template
reg = NodeParams(IterREGBET(),
Expand Down Expand Up @@ -2412,10 +2417,10 @@ def create_full_ants_subpipes(
outputnode, "masked_debiased_T1")

else:
print("Using reg_aladin transfo to pad masked_debiased_T1 back")
print("Using reg_aladin transfo to pad masked_debiased_T1")

pad_masked_debiased_T1 = pe.Node(RegResample(),
name="pad_masked_debiased_T1")
name="pad_masked_debiased_T1")

seg_pipe.connect(brain_segment_pipe,
"outputnode.masked_debiased_T1",
Expand Down Expand Up @@ -2490,10 +2495,10 @@ def create_full_ants_subpipes(
outputnode, "masked_debiased_T2")

else:
print("Using reg_aladin transfo to pad masked_debiased_T2 back")
print("Using reg_aladin transfo to pad masked_debiased_T2")

pad_masked_debiased_T2 = pe.Node(RegResample(),
name="pad_masked_debiased_T2")
name="pad_masked_debiased_T2")

seg_pipe.connect(brain_segment_pipe,
"outputnode.masked_debiased_T2",
Expand Down Expand Up @@ -2804,7 +2809,8 @@ def create_full_ants_subpipes(

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

seg_pipe.connect(native_to_stereo_pipe,
'outputnode.stereo_native_T1',
Expand Down Expand Up @@ -2920,7 +2926,7 @@ def create_full_ants_subpipes(
apply_stereo_native_T2, "ref_file")

seg_pipe.connect(apply_stereo_native_T2, "out_file",
outputnode, "stereo_native_T2")
outputnode, "stereo_native_T2")

if pad:

Expand Down Expand Up @@ -3940,10 +3946,10 @@ def create_full_T1_ants_subpipes(params_template, params_template_aladin,
outputnode, "masked_debiased_T1")

else:
print("Using reg_aladin transfo to pad masked_debiased_T1 back")
print("Using reg_aladin transfo to pad masked_debiased_T1")

pad_masked_debiased_T1 = pe.Node(RegResample(),
name="pad_masked_debiased_T1")
name="pad_masked_debiased_T1")

seg_pipe.connect(brain_segment_pipe,
"outputnode.masked_debiased_T1",
Expand Down
8 changes: 4 additions & 4 deletions macapype/pipelines/prepare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -589,10 +589,10 @@ def create_short_preparation_pipe(params, params_template={},
# outputnode
if "avg_reorient_pipe" in params.keys():
data_preparation_pipe.connect(av_T1, 'outputnode.std_img',
outputnode, 'native_T1')
outputnode, 'native_T1')
else:
data_preparation_pipe.connect(av_T1, 'avg_img',
outputnode, 'native_T1')
outputnode, 'native_T1')

if 'aladin_T2_on_T1' in params.keys():
data_preparation_pipe.connect(align_T2_on_T1, "res_file",
Expand Down Expand Up @@ -1064,10 +1064,10 @@ def create_short_preparation_T1_pipe(params, params_template,

if "avg_reorient_pipe" in params.keys():
data_preparation_pipe.connect(av_T1, 'outputnode.std_img',
crop_aladin_T1, 'flo_file')
crop_aladin_T1, 'flo_file')
else:
data_preparation_pipe.connect(av_T1, 'avg_img',
crop_aladin_T1, 'flo_file')
crop_aladin_T1, 'flo_file')

# compute inv transfo
inv_tranfo = NodeParams(
Expand Down
22 changes: 8 additions & 14 deletions macapype/pipelines/segment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

import nipype.interfaces.spm as spm

from ..nodes.segment import (AtroposN4, merge_masks, BinaryFillHoles,
from ..nodes.segment import (AtroposN4, merge_masks,
merge_imgs, split_indexed_mask, copy_header,
compute_5tt, fill_list_vol)

Expand Down Expand Up @@ -753,30 +753,25 @@ def create_native_old_segment_seg_pipe(params_template, params={},
register_tissue_to_nat.inputs.output_type = "NIFTI" # for SPM segment
register_tissue_to_nat.inputs.interp = "nearestneighbour"


seg_pipe.connect(split_seg, 'list_split_files',
register_tissue_to_nat, 'in_file')
register_tissue_to_nat, 'in_file')

# joining (Merge)

# Segment in to 6 tissues
segment = NodeParams(spm.Segment(),
params=parse_key(params, "segment"),
name="old_segment")

seg_pipe.connect(merge_tissue_files, "out",
segment, "tissue_prob_maps")
params=parse_key(params, "segment"),
name="old_segment")

seg_pipe.connect(unzip, 'unzipped_file', segment, 'data')


segment = pe.JoinNode(interface=spm.Segment(),
joinsource="register_tissue_to_nat",
joinfield="tissue_prob_maps",
name="old_segment")
joinsource="register_tissue_to_nat",
joinfield="tissue_prob_maps",
name="old_segment")

seg_pipe.connect(register_tissue_to_nat, "out_file",
segment, "tissue_prob_maps")
segment, "tissue_prob_maps")

seg_pipe.connect(unzip, 'unzipped_file', segment, 'data')

Expand Down Expand Up @@ -851,7 +846,6 @@ def create_native_old_segment_pipe(params_template, params={},
assert set_spm(), \
"Error, SPM was not found, cannot run SPM old segment pipeline"


# gm
register_gm_to_nat = pe.Node(fsl.ApplyXFM(), name="register_gm_to_nat")
register_gm_to_nat.inputs.output_type = "NIFTI" # for SPM segment
Expand Down
16 changes: 10 additions & 6 deletions macapype/utils/utils_params.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,10 @@
import json
import pprint


def update_preparation_params(ssoft=[], subjects=None, sessions=None,
params=None, indiv_params=None, extra_wf_name=""):
params=None, indiv_params=None,
extra_wf_name=""):

if "short_preparation_pipe" not in params.keys():

Expand All @@ -21,7 +23,7 @@ def update_preparation_params(ssoft=[], subjects=None, sessions=None,
count_long_crops = 0
count_multi_long_crops = 0

if subjects is None :
if subjects is None:
print("For whole BIDS dir, \
unable to assess if the indiv_params is correct")
print("Running by default short_preparation_pipe and crop_T1")
Expand All @@ -39,8 +41,8 @@ def update_preparation_params(ssoft=[], subjects=None, sessions=None,
sub.split('-')[1], subjects))
continue


if all([key.split('-')[0] == "ses" for key in indiv_params[sub].keys()]):
if all([key.split('-')[0] == "ses"
for key in indiv_params[sub].keys()]):

for ses in indiv_params[sub].keys():

Expand Down Expand Up @@ -91,7 +93,6 @@ def update_preparation_params(ssoft=[], subjects=None, sessions=None,

count_multi_long_crops += 1


print("count_all_sessions {}".format(count_all_sessions))
print("count_T1_crops {}".format(count_T1_crops))
print("count_long_crops {}".format(count_long_crops))
Expand Down Expand Up @@ -181,6 +182,7 @@ def update_preparation_params(ssoft=[], subjects=None, sessions=None,

return params, indiv_params, extra_wf_name


def update_params(ssoft=[], subjects=None, sessions=None,
params_file=None, indiv_params_file=None):

Expand Down Expand Up @@ -221,7 +223,9 @@ def update_params(ssoft=[], subjects=None, sessions=None,

pprint.pprint(indiv_params)

params, indiv_params, extra_wf_name = update_preparation_params(ssoft, subjects=subjects, sessions=sessions, indiv_params=indiv_params, params=params, extra_wf_name="")
params, indiv_params, extra_wf_name = update_preparation_params(
ssoft, subjects=subjects, sessions=sessions,
indiv_params=indiv_params, params=params, extra_wf_name="")

# prep for testing only preparation part
if "prep" in ssoft:
Expand Down

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