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🩹 Distortion correction: ~~el~~if (#1804)
2 parents a938dc4 + ee72598 commit c28ff76

12 files changed

+17
-567
lines changed

‎CPAC/distortion_correction/utils.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -183,24 +183,24 @@ def phase_encode(unwarp_dir, phase_one, phase_two, dwell_time_one=None,
183183
if isinstance(unwarp_dir, bytes):
184184
unwarp_dir = unwarp_dir.decode()
185185

186-
if unwarp_dir in ["x", "x-", "-x","i","-i","i-"]:
186+
if unwarp_dir in ["x", "x-", "-x", "i", "-i", "i-"]:
187187
if dwell_time_one and dwell_time_two:
188188
dim = nibabel.load(phase_one).shape[0]
189189
n_PE_steps = dim - 1
190190
ro_time_one = np.round(dwell_time_one * n_PE_steps, 6)
191191
ro_time_two = np.round(dwell_time_two * n_PE_steps, 6)
192-
elif ro_time_one and ro_time_two:
192+
if ro_time_one and ro_time_two:
193193
ro_times = [f"-1 0 0 {ro_time_one}", f"1 0 0 {ro_time_two}"]
194194
else:
195195
raise Exception("[!] No dwell time or total readout time "
196196
"present for the acq-fMRI EPI field maps.")
197-
elif unwarp_dir in ["y", "y-", "-y","j","-j","j-"]:
197+
elif unwarp_dir in ["y", "y-", "-y", "j", "-j", "j-"]:
198198
if dwell_time_one and dwell_time_two:
199199
dim = nibabel.load(phase_one).shape[1]
200200
n_PE_steps = dim - 1
201201
ro_time_one = np.round(dwell_time_one * n_PE_steps, 6)
202202
ro_time_two = np.round(dwell_time_two * n_PE_steps, 6)
203-
elif ro_time_one and ro_time_two:
203+
if ro_time_one and ro_time_two:
204204
ro_times = [f"0 -1 0 {ro_time_one}", f"0 1 0 {ro_time_two}"]
205205
else:
206206
raise Exception("[!] No dwell time or total readout time "

‎CPAC/resources/configs/pipeline_config_abcd-options.yml‎

Lines changed: 0 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -97,13 +97,6 @@ registration_workflows:
9797
# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
9898
T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz
9999

100-
# Reference mask for FSL registration.
101-
ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
102-
103-
# Identity matrix used during FSL-based resampling of anatomical-space data throughout the pipeline.
104-
# It is not necessary to change this path unless you intend to use a different template.
105-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
106-
107100
# option parameters
108101
ANTs:
109102

@@ -183,10 +176,6 @@ registration_workflows:
183176
# It is not necessary to change this path unless you intend to use a non-standard template.
184177
T1w_brain_template: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_${resolution_for_anat}_brain.nii.gz
185178

186-
# Template to be used during registration.
187-
# It is not necessary to change this path unless you intend to use a non-standard template.
188-
T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
189-
190179
# Template to be used during registration.
191180
# It is not necessary to change this path unless you intend to use a non-standard template.
192181
T1w_brain_template_mask: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
@@ -205,12 +194,6 @@ registration_workflows:
205194
# input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
206195
input: [Selected_Functional_Volume]
207196

208-
boundary_based_registration:
209-
210-
# Standard FSL 5.0 Scheduler used for Boundary Based Registration.
211-
# It is not necessary to change this path unless you intend to use non-standard MNI registration.
212-
bbr_schedule: $FSLDIR/etc/flirtsch/bbr.sch
213-
214197
# reference: 'brain' or 'restore-brain'
215198
# In ABCD-options pipeline, 'restore-brain' is used as coregistration reference
216199
reference: restore-brain
@@ -274,19 +257,6 @@ registration_workflows:
274257
# Possible values: Linear, BSpline, LanczosWindowedSinc
275258
interpolation: Linear
276259

277-
FNIRT_pipelines:
278-
279-
# Identity matrix used during FSL-based resampling of functional-space data throughout the pipeline.
280-
# It is not necessary to change this path unless you intend to use a different template.
281-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
282-
283-
EPI_registration:
284-
FSL-FNIRT:
285-
286-
# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
287-
# It is not necessary to change this path unless you intend to use a different template.
288-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
289-
290260
functional_preproc:
291261
run: On
292262
motion_estimates_and_correction:
@@ -321,9 +291,6 @@ functional_preproc:
321291
using: [PhaseDiff, Blip-FSL-TOPUP]
322292

323293
func_masking:
324-
FSL_AFNI:
325-
brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
326-
brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
327294

328295
# Apply functional mask in native space
329296
apply_func_mask_in_native_space: Off

‎CPAC/resources/configs/pipeline_config_anat-only.yml‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -77,15 +77,15 @@ registration_workflows:
7777
FSL-FNIRT:
7878

7979
# Reference mask for FSL registration.
80-
ref_mask: $$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
80+
ref_mask: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
8181

8282
# Template to be used during registration.
8383
# It is not necessary to change this path unless you intend to use a non-standard template.
84-
T1w_brain_template: $$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
84+
T1w_brain_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
8585

8686
# Template to be used during registration.
8787
# It is not necessary to change this path unless you intend to use a non-standard template.
88-
T1w_template: $$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
88+
T1w_template: $$$FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
8989

9090
# Register skull-on anatomical image to a template.
9191
reg_with_skull: Off
@@ -112,11 +112,11 @@ registration_workflows:
112112

113113
# Standard Skull Stripped Template. Used as a reference image for functional registration.
114114
# This can be different than the template used as the reference/fixed for T1-to-template registration.
115-
T1w_brain_template_funcreg: $$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
115+
T1w_brain_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
116116

117117
# Standard Anatomical Brain Image with Skull.
118118
# This can be different than the template used as the reference/fixed for T1-to-template registration.
119-
T1w_template_funcreg: $$FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
119+
T1w_template_funcreg: $$$FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
120120

121121
EPI_registration:
122122
ANTs:
@@ -129,7 +129,7 @@ registration_workflows:
129129

130130
# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
131131
# It is not necessary to change this path unless you intend to use a different template.
132-
identity_matrix: $$FSLDIR/etc/flirtsch/ident.mat
132+
identity_matrix: $$$FSLDIR/etc/flirtsch/ident.mat
133133

134134
functional_preproc:
135135
run: Off

‎CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml‎

Lines changed: 0 additions & 67 deletions
Original file line numberDiff line numberDiff line change
@@ -73,9 +73,6 @@ anatomical_preproc:
7373
acpc_alignment:
7474
T1w_brain_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
7575

76-
# ACPC aligned template
77-
T1w_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
78-
7976
brain_extraction:
8077
run: On
8178
FSL-BET:
@@ -100,33 +97,6 @@ segmentation:
10097
registration_workflows:
10198
anatomical_registration:
10299
run: On
103-
registration:
104-
FSL-FNIRT:
105-
106-
# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
107-
ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
108-
109-
# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
110-
T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
111-
112-
# Reference mask for FSL registration.
113-
ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
114-
115-
# Identity matrix used during FSL-based resampling of anatomical-space data throughout the pipeline.
116-
# It is not necessary to change this path unless you intend to use a different template.
117-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
118-
119-
# Template to be used during registration.
120-
# It is not necessary to change this path unless you intend to use a non-standard template.
121-
T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
122-
123-
# Template to be used during registration.
124-
# It is not necessary to change this path unless you intend to use a non-standard template.
125-
T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
126-
127-
# Template to be used during registration.
128-
# It is not necessary to change this path unless you intend to use a non-standard template.
129-
T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
130100

131101
# Register skull-on anatomical image to a template.
132102
reg_with_skull: Off
@@ -142,10 +112,6 @@ registration_workflows:
142112
# run: [On, Off] - this will run both and fork the pipeline
143113
run: [On]
144114

145-
# Standard FSL 5.0 Scheduler used for Boundary Based Registration.
146-
# It is not necessary to change this path unless you intend to use non-standard MNI registration.
147-
bbr_schedule: $FSLDIR/etc/flirtsch/bbr.sch
148-
149115
func_registration_to_template:
150116

151117
# these options modify the application (to the functional data), not the calculation, of the
@@ -160,34 +126,6 @@ registration_workflows:
160126
# thus, a higher resolution may not result in a large increase in RAM needs as above
161127
func_derivative_outputs: 2mm
162128

163-
target_template:
164-
T1_template:
165-
166-
# Standard Skull Stripped Template. Used as a reference image for functional registration.
167-
# This can be different than the template used as the reference/fixed for T1-to-template registration.
168-
T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
169-
170-
# Standard Anatomical Brain Image with Skull.
171-
# This can be different than the template used as the reference/fixed for T1-to-template registration.
172-
T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
173-
174-
# Template to be used during registration.
175-
# It is not necessary to change this path unless you intend to use a non-standard template.
176-
T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
177-
178-
FNIRT_pipelines:
179-
180-
# Identity matrix used during FSL-based resampling of functional-space data throughout the pipeline.
181-
# It is not necessary to change this path unless you intend to use a different template.
182-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
183-
184-
EPI_registration:
185-
FSL-FNIRT:
186-
187-
# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
188-
# It is not necessary to change this path unless you intend to use a different template.
189-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
190-
191129
functional_preproc:
192130
run: On
193131
slice_timing_correction:
@@ -206,11 +144,6 @@ functional_preproc:
206144
# run: [On, Off] - this will run both and fork the pipeline
207145
run: [On]
208146

209-
func_masking:
210-
FSL_AFNI:
211-
brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
212-
brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
213-
214147
generate_func_mean:
215148

216149
# Generate mean functional image

‎CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml‎

Lines changed: 0 additions & 65 deletions
Original file line numberDiff line numberDiff line change
@@ -78,9 +78,6 @@ anatomical_preproc:
7878
acpc_alignment:
7979
T1w_brain_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
8080

81-
# ACPC aligned template
82-
T1w_ACPC_template: $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
83-
8481
brain_extraction:
8582
run: On
8683

@@ -106,20 +103,6 @@ registration_workflows:
106103
anatomical_registration:
107104
run: On
108105
registration:
109-
FSL-FNIRT:
110-
111-
# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
112-
ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
113-
114-
# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
115-
T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
116-
117-
# Reference mask for FSL registration.
118-
ref_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask_dil.nii.gz
119-
120-
# Identity matrix used during FSL-based resampling of anatomical-space data throughout the pipeline.
121-
# It is not necessary to change this path unless you intend to use a different template.
122-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
123106

124107
# using: ['ANTS', 'FSL', 'FSL-linear']
125108
# this is a fork point
@@ -132,18 +115,6 @@ registration_workflows:
132115
# ANTs parameters for T1-template-based registration
133116
T1_registration:
134117

135-
# Template to be used during registration.
136-
# It is not necessary to change this path unless you intend to use a non-standard template.
137-
T1w_brain_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain.nii.gz
138-
139-
# Template to be used during registration.
140-
# It is not necessary to change this path unless you intend to use a non-standard template.
141-
T1w_template: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}.nii.gz
142-
143-
# Template to be used during registration.
144-
# It is not necessary to change this path unless you intend to use a non-standard template.
145-
T1w_brain_template_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
146-
147118
# Register skull-on anatomical image to a template.
148119
reg_with_skull: Off
149120

@@ -158,10 +129,6 @@ registration_workflows:
158129
# run: [On, Off] - this will run both and fork the pipeline
159130
run: [On]
160131

161-
# Standard FSL 5.0 Scheduler used for Boundary Based Registration.
162-
# It is not necessary to change this path unless you intend to use non-standard MNI registration.
163-
bbr_schedule: $FSLDIR/etc/flirtsch/bbr.sch
164-
165132
func_registration_to_template:
166133

167134
# these options modify the application (to the functional data), not the calculation, of the
@@ -176,40 +143,13 @@ registration_workflows:
176143
# thus, a higher resolution may not result in a large increase in RAM needs as above
177144
func_derivative_outputs: 2mm
178145

179-
target_template:
180-
T1_template:
181-
182-
# Standard Skull Stripped Template. Used as a reference image for functional registration.
183-
# This can be different than the template used as the reference/fixed for T1-to-template registration.
184-
T1w_brain_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain.nii.gz
185-
186-
# Standard Anatomical Brain Image with Skull.
187-
# This can be different than the template used as the reference/fixed for T1-to-template registration.
188-
T1w_template_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}.nii.gz
189-
190-
# Template to be used during registration.
191-
# It is not necessary to change this path unless you intend to use a non-standard template.
192-
T1w_brain_template_mask_funcreg: $FSLDIR/data/standard/MNI152_T1_${func_resolution}_brain_mask.nii.gz
193-
194-
FNIRT_pipelines:
195-
196-
# Identity matrix used during FSL-based resampling of functional-space data throughout the pipeline.
197-
# It is not necessary to change this path unless you intend to use a different template.
198-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
199-
200146
EPI_registration:
201147
ANTs:
202148

203149
# EPI registration configuration - synonymous with T1_registration
204150
# parameters under anatomical registration above
205151
parameters:
206152

207-
FSL-FNIRT:
208-
209-
# Identity matrix used during FSL-based resampling of BOLD-space data throughout the pipeline.
210-
# It is not necessary to change this path unless you intend to use a different template.
211-
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat
212-
213153
functional_preproc:
214154
run: On
215155
slice_timing_correction:
@@ -228,11 +168,6 @@ functional_preproc:
228168
# run: [On, Off] - this will run both and fork the pipeline
229169
run: [On]
230170

231-
func_masking:
232-
FSL_AFNI:
233-
brain_mask: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
234-
brain_probseg: $FSLDIR/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
235-
236171
generate_func_mean:
237172

238173
# Generate mean functional image

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