🔀 Merge develop into apply-filter-more-broadly

FCP-INDI · Jul 21, 2023 · 7f87df2 · 7f87df2
2 parents fda6343 + bb4c00c
commit 7f87df2
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Showing 20 changed files with 154 additions and 50 deletions.
diff --git a/CPAC/func_preproc/func_motion.py b/CPAC/func_preproc/func_motion.py
@@ -38,25 +38,15 @@
 
 
 @nodeblock(
-    name="calc_motion_stats",
-    switch=[["functional_preproc", "run"],
-            ["functional_preproc", "motion_estimates_and_correction",
-             "motion_estimates", "calculate_motion_after"]],
-    inputs=[("desc-preproc_bold",
-             "space-bold_desc-brain_mask",
-             "max-displacement",
-             "rels-displacement",
-             "movement-parameters",
-             ["filtered-movement-parameters", "movement-parameters"],
-             ["filtered-coordinate-transformation",
-             "coordinate-transformation"]),
-            "subject",
-            "scan"],
-     outputs=["framewise-displacement-power",
-              "framewise-displacement-jenkinson",
-              "dvars",
-              "power-params",
-              "motion-params"])
+    name='calc_motion_stats',
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'motion_estimates_and_correction', 'run'],
+            ['functional_preproc', 'motion_estimates_and_correction', 'motion_estimates', 'calculate_motion_after']],
+    inputs=[('desc-preproc_bold', 'space-bold_desc-brain_mask', 'movement-parameters', 'max-displacement',
+             'rels-displacement', 'coordinate-transformation'), 'subject', 'scan'],
+    outputs=['framewise-displacement-power', 'framewise-displacement-jenkinson', 'dvars', 'power-params',
+             'motion-params']
+)
 def calc_motion_stats(wf, cfg, strat_pool, pipe_num, opt=None):
     '''Calculate motion statistics for motion parameters.'''
     motion_prov = strat_pool.get_cpac_provenance('movement-parameters')

diff --git a/CPAC/func_preproc/func_preproc.py b/CPAC/func_preproc/func_preproc.py
@@ -513,11 +513,12 @@ def get_idx(in_files, stop_idx=None, start_idx=None):
 
 
 @nodeblock(
-    name="func_reorient",
-    config=["functional_preproc"],
-    switch=["run"],
-    inputs=["bold"],
-    outputs=["desc-preproc_bold", "desc-reorient_bold"])
+    name='func_reorient',
+    config=['functional_preproc'],
+    switch=['run'],
+    inputs=['bold'],
+    outputs=['desc-preproc_bold', 'desc-reorient_bold']
+)
 def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
 
     func_deoblique = pe.Node(interface=afni_utils.Refit(),
@@ -724,9 +725,9 @@ def func_slice_time(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_mask_afni',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='AFNI',
     inputs=['desc-preproc_bold'],
     outputs={'space-bold_desc-brain_mask':
@@ -750,9 +751,9 @@ def bold_mask_afni(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_mask_fsl',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='FSL',
     inputs=['desc-preproc_bold'],
     outputs=['space-bold_desc-brain_mask']
@@ -903,9 +904,9 @@ def form_thr_string(thr):
 
 @nodeblock(
     name='bold_mask_fsl_afni',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='FSL_AFNI',
     inputs=[('motion-basefile', 'desc-preproc_bold'), 'FSL-AFNI-bold-ref', 'FSL-AFNI-brain-mask',
             'FSL-AFNI-brain-probseg'],
@@ -1081,9 +1082,9 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_mask_anatomical_refined',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='Anatomical_Refined',
     inputs=[('bold', 'desc-preproc_bold'),
             ('desc-brain_T1w', ['space-T1w_desc-brain_mask', 'space-T1w_desc-acpcbrain_mask'])],
@@ -1200,9 +1201,9 @@ def bold_mask_anatomical_refined(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_mask_anatomical_based',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='Anatomical_Based',
     inputs=['desc-preproc_bold', ('desc-brain_T1w', ['desc-preproc_T1w', 'desc-reorient_T1w', 'T1w'])],
     outputs=['space-bold_desc-brain_mask']
@@ -1292,9 +1293,9 @@ def bold_mask_anatomical_based(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_mask_anatomical_resampled',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='Anatomical_Resampled',
     inputs=['desc-preproc_bold', 'T1w-template-funcreg', 'space-template_desc-preproc_T1w',
             'space-template_desc-T1w_mask'],
@@ -1361,9 +1362,9 @@ def bold_mask_anatomical_resampled(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_mask_ccs',
-    config=['functional_preproc'],
-    switch=['run'],
-    option_key=['func_masking', 'using'],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run']],
+    option_key=['functional_preproc', 'func_masking', 'using'],
     option_val='CCS_Anatomical_Refined',
     inputs=[['desc-motion_bold', 'desc-preproc_bold', 'bold'], 'desc-brain_T1w',
             ['desc-preproc_T1w', 'desc-reorient_T1w', 'T1w']],
@@ -1503,8 +1504,9 @@ def bold_mask_ccs(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name='bold_masking',
-    config=None,
-    switch=[['functional_preproc', 'run'], ['functional_preproc', 'func_masking', 'apply_func_mask_in_native_space']],
+    switch=[['functional_preproc', 'run'],
+            ['functional_preproc', 'func_masking', 'run'],
+            ['functional_preproc', 'func_masking', 'apply_func_mask_in_native_space']],
     inputs=[('desc-preproc_bold', 'space-bold_desc-brain_mask')],
     outputs={'desc-preproc_bold': {'Description': 'The skull-stripped BOLD time-series.', 'SkullStripped': True},
              'desc-brain_bold': {'Description': 'The skull-stripped BOLD time-series.', 'SkullStripped': True}}

diff --git a/CPAC/pipeline/schema.py b/CPAC/pipeline/schema.py
@@ -813,6 +813,7 @@ def sanitize(filename):
             }
         },
         'func_masking': {
+            'run': bool1_1,
             'using': [In(
                 ['AFNI', 'FSL', 'FSL_AFNI', 'Anatomical_Refined',
                  'Anatomical_Based', 'Anatomical_Resampled',
@@ -855,6 +856,9 @@ def sanitize(filename):
         'normalize_func': {
             'run': bool1_1,
         },
+        'coreg_prep': {
+            'run': bool1_1,
+        },
     },
     'nuisance_corrections': {
         '1-ICA-AROMA': {

diff --git a/CPAC/registration/registration.py b/CPAC/registration/registration.py
@@ -2854,7 +2854,8 @@ def coregistration_prep_vol(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name="coregistration_prep_mean",
-    switch=["functional_preproc", "run"],
+    switch=[["functional_preproc", "run"],
+            ["functional_preproc", "coreg_prep", "run"]],
     option_key=[
         "registration_workflows",
         "functional_registration",
@@ -2897,7 +2898,8 @@ def coregistration_prep_mean(wf, cfg, strat_pool, pipe_num, opt=None):
 
 @nodeblock(
     name="coregistration_prep_fmriprep",
-    switch=["functional_preproc", "run"],
+    switch=[["functional_preproc", "run"],
+            ["functional_preproc", "coreg_prep", "run"]],
     option_key=[
         "registration_workflows",
         "functional_registration",

diff --git a/CPAC/resources/configs/pipeline_config_abcd-options.yml b/CPAC/resources/configs/pipeline_config_abcd-options.yml
@@ -295,6 +295,7 @@ functional_preproc:
     using: [PhaseDiff, Blip-FSL-TOPUP]
 
   func_masking:
+    run: On
 
     # Apply functional mask in native space
     apply_func_mask_in_native_space: Off
@@ -313,6 +314,11 @@ functional_preproc:
     # Generate mean functional image
     run: On
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml b/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml
@@ -144,6 +144,9 @@ functional_preproc:
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
 
+  func_masking:
+    run: On
+
   generate_func_mean:
 
     # Generate mean functional image
@@ -154,6 +157,11 @@ functional_preproc:
     # Normalize functional image
     run: On
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml b/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml
@@ -168,6 +168,9 @@ functional_preproc:
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
 
+  func_masking:
+    run: On
+
   generate_func_mean:
 
     # Generate mean functional image
@@ -178,6 +181,11 @@ functional_preproc:
     # Normalize functional image
     run: On
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_blank.yml b/CPAC/resources/configs/pipeline_config_blank.yml
@@ -1060,6 +1060,7 @@ functional_preproc:
       fmap_skullstrip_AFNI_threshold: 0.6
 
   func_masking:
+    run: Off
     FSL-BET:
 
       # Set an intensity threshold to improve skull stripping performances of FSL BET on rodent scans.
@@ -1172,6 +1173,11 @@ functional_preproc:
     run: [Off]
     space: native
 
+  coreg_prep:
+
+    # Generate sbref
+    run: Off
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_ccs-options.yml b/CPAC/resources/configs/pipeline_config_ccs-options.yml
@@ -171,6 +171,7 @@ functional_preproc:
     run: [On]
 
   func_masking:
+    run: On
 
     # using: ['AFNI', 'FSL', 'FSL_AFNI', 'Anatomical_Refined', 'Anatomical_Based', 'Anatomical_Resampled', 'CCS_Anatomical_Refined']
     # FSL_AFNI: fMRIPrep-style BOLD mask. Ref: https://github.com/nipreps/niworkflows/blob/a221f612/niworkflows/func/util.py#L246-L514
@@ -198,6 +199,11 @@ functional_preproc:
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_default-deprecated.yml b/CPAC/resources/configs/pipeline_config_default-deprecated.yml
@@ -75,6 +75,9 @@ functional_preproc:
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
 
+  func_masking:
+    run: On
+
   generate_func_mean:
 
     # Generate mean functional image
@@ -85,6 +88,11 @@ functional_preproc:
     # Normalize functional image
     run: On
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_default.yml b/CPAC/resources/configs/pipeline_config_default.yml
@@ -1247,7 +1247,7 @@ functional_preproc:
       regrid: 1
 
   func_masking:
-
+    run: On
     # using: ['AFNI', 'FSL', 'FSL_AFNI', 'Anatomical_Refined', 'Anatomical_Based', 'Anatomical_Resampled', 'CCS_Anatomical_Refined']
 
     # FSL_AFNI: fMRIPrep-style BOLD mask. Ref: https://github.com/nipreps/niworkflows/blob/a221f612/niworkflows/func/util.py#L246-L514
@@ -1335,7 +1335,11 @@ functional_preproc:
 
     # Normalize functional image
     run: On
+
+  coreg_prep:
 
+    # Generate sbref
+    run: On
 
 nuisance_corrections:
 

diff --git a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml
@@ -368,6 +368,7 @@ functional_preproc:
     run: [On]
 
   func_masking:
+    run: On
     FSL_AFNI:
       bold_ref: /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz
       brain_mask: /code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
@@ -387,6 +388,11 @@ functional_preproc:
     # Generate mean functional image
     run: On
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression:
 

diff --git a/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml b/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml
@@ -326,6 +326,7 @@ functional_preproc:
     using: []
 
   func_masking:
+    run: On
     FSL_AFNI:
       brain_mask: /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
       brain_probseg: /usr/share/fsl/5.0/data/standard/MNI152_T1_${resolution_for_anat}_brain_mask.nii.gz
@@ -349,6 +350,11 @@ functional_preproc:
     # Normalize functional image
     run: On
 
+  coreg_prep:
+
+    # Generate sbref
+    run: On
+
 nuisance_corrections:
   2-nuisance_regression: