Merge pull request #1884 from nx10/develop-1.8.6

Merge branch 'develop' into develop-1.8.6

Author: nx10

CHANGELOG.md

@@ -27,6 +27,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added `fail_fast` configuration setting and CLI flag
 - Added abililty to fork on motion filter
 - Added [`sdcflows`](https://www.nipreps.org/sdcflows/2.0/) to CPAC requirements
+- Added the ability to ingress FreeSurfer data into CPAC
+- Added the ability to toggle FreeSurfer derived masks for brain extraction
 
 ### Changed
 - Freesurfer output directory ingress moved to the data configuration YAML
@@ -66,6 +68,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed a bug where ALFF & f/ALFF would not run if frequency filtering was disabled earlier in the pipeline.
 - Fixed a bug where `surface_analysis.freesurfer.freesurfer_dir` in the pipeline config was not ingressed at runtime.
 - Added public read access to some overly restricted packaged templates
+- Fixed a bug where notch filter was always assuming the sampling frequency was `2.0`.
 
 ## [v1.8.4] - 2022-06-27
 

CPAC/anat_preproc/anat_preproc.py

@@ -174,22 +174,22 @@ def split_hemi_interface():
     for label in splits:
         wf.connect(reconall, label, splits[label], 'multi_file')
     outputs = {
-        'hemi-L_desc-surface_curv': (splits['curv'], 'lh'),
-        'hemi-R_desc-surface_curv': (splits['curv'], 'rh'),
-        'hemi-L_desc-surfaceMesh_pial': (splits['pial'], 'lh'),
-        'hemi-R_desc-surfaceMesh_pial': (splits['pial'], 'rh'),
-        'hemi-L_desc-surfaceMesh_smoothwm': (splits['smoothwm'], 'lh'),
-        'hemi-R_desc-surfaceMesh_smoothwm': (splits['smoothwm'], 'rh'),
-        'hemi-L_desc-surfaceMesh_sphere': (splits['sphere'], 'lh'),
-        'hemi-R_desc-surfaceMesh_sphere': (splits['sphere'], 'rh'),
-        'hemi-L_desc-surfaceMap_sulc': (splits['sulc'], 'lh'),
-        'hemi-R_desc-surfaceMap_sulc': (splits['sulc'], 'rh'),
-        'hemi-L_desc-surfaceMap_thickness': (splits['thickness'], 'lh'),
-        'hemi-R_desc-surfaceMap_thickness': (splits['thickness'], 'rh'),
-        'hemi-L_desc-surfaceMap_volume': (splits['volume'], 'lh'),
-        'hemi-R_desc-surfaceMap_volume': (splits['volume'], 'rh'),
-        'hemi-L_desc-surfaceMesh_white': (splits['white'], 'lh'),
-        'hemi-R_desc-surfaceMesh_white': (splits['white'], 'rh')}
+        'pipeline-fs_hemi-L_desc-surface_curv': (splits['curv'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surface_curv': (splits['curv'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMesh_pial': (splits['pial'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMesh_pial': (splits['pial'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMesh_smoothwm': (splits['smoothwm'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMesh_smoothwm': (splits['smoothwm'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMesh_sphere': (splits['sphere'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMesh_sphere': (splits['sphere'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMap_sulc': (splits['sulc'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMap_sulc': (splits['sulc'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMap_thickness': (splits['thickness'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMap_thickness': (splits['thickness'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMap_volume': (splits['volume'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMap_volume': (splits['volume'], 'rh'),
+        'pipeline-fs_hemi-L_desc-surfaceMesh_white': (splits['white'], 'lh'),
+        'pipeline-fs_hemi-R_desc-surfaceMesh_white': (splits['white'], 'rh')}
 
     return wf, outputs
 

CPAC/anat_preproc/utils.py

@@ -1,11 +1,26 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+# Copyright (C) 2021-2023  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functions for creating connectome connectivity matrices."""
 import os
 from warnings import warn
 import numpy as np
 from nilearn.connectome import ConnectivityMeasure
-from nilearn.input_data import NiftiLabelsMasker
 from nipype import logging
 from nipype.interfaces import utility as util
 from CPAC.pipeline import nipype_pipeline_engine as pe
@@ -99,17 +114,22 @@ def compute_connectome_nilearn(in_rois, in_file, method, atlas_name):
     -------
     numpy.ndarray or NotImplemented
     """
+    from nilearn.input_data import NiftiLabelsMasker
+    from nipype.utils.tmpdirs import TemporaryDirectory
     tool = 'Nilearn'
     output = connectome_name(atlas_name, tool, method)
     method = get_connectome_method(method, tool)
     if method is NotImplemented:
         return NotImplemented
-    masker = NiftiLabelsMasker(labels_img=in_rois,
-                               standardize=True,
-                               verbose=True)
-    timeser = masker.fit_transform(in_file)
-    correlation_measure = ConnectivityMeasure(kind=method)
-    corr_matrix = correlation_measure.fit_transform([timeser])[0]
+    with TemporaryDirectory() as cache_dir:
+        masker = NiftiLabelsMasker(labels_img=in_rois,
+                                standardize=True,
+                                verbose=True,
+                                memory=cache_dir,
+                                memory_level=3)
+        timeser = masker.fit_transform(in_file)
+        correlation_measure = ConnectivityMeasure(kind=method)
+        corr_matrix = correlation_measure.fit_transform([timeser])[0]
     np.fill_diagonal(corr_matrix, 1)
     np.savetxt(output, corr_matrix, delimiter='\t')
     return output

CPAC/connectome/connectivity_matrix.py

@@ -163,7 +163,7 @@ def notch_filter_motion(motion_params, filter_type, TR, fc_RR_min=None,
         bandwidth = fa[1] - fa[0]
 
         Q = Wn/bw
-        [b_filt, a_filt] = iirnotch(Wn, Q)
+        [b_filt, a_filt] = iirnotch(Wn, Q, fs)
         num_f_apply = np.floor(filter_order / 2)
 
         filter_info = f"Motion estimate filter information\n\nType: Notch\n" \

CPAC/func_preproc/utils.py

@@ -1,3 +1,19 @@
+# Copyright (C) 2012-2023  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 import re
 import os
 import numpy as np
@@ -2455,8 +2471,9 @@ def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt, space, res=None):
                                        '2-nuisance_regression',
                                        'bandpass_filtering_order'] == 'Before'
 
-    name_suff = (f'{space}_{opt["Name"]}_{pipe_num}' if res is None else
-                 f'{space}_res-{res}_{opt["Name"]}_{pipe_num}')
+    name_suff = (f'space-{space}_reg-{opt["Name"]}_{pipe_num}'
+                 if res is None else
+                 f'space-{space}_res-{res}_reg-{opt["Name"]}_{pipe_num}')
     nuis_name = f'nuisance_regression_{name_suff}'
 
     nuis = create_nuisance_regression_workflow(opt, name=nuis_name)
@@ -2475,7 +2492,8 @@ def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt, space, res=None):
         # sometimes mm dimensions match but the voxel dimensions don't
         # so here we align the mask to the resampled data before applying
         match_grid = pe.Node(afni.Resample(),
-                             name='align_template_mask_to_template_data')
+                             name='align_template_mask_to_template_data_'
+                                  f'{name_suff}')
         match_grid.inputs.outputtype = 'NIFTI_GZ'
         match_grid.inputs.resample_mode = 'Cu'
         node, out = strat_pool.get_data('FSL-AFNI-brain-mask')
@@ -2626,6 +2644,7 @@ def nuisance_regression_template(wf, cfg, strat_pool, pipe_num, opt=None):
      "inputs": [("desc-stc_bold",
                  "space-template_desc-preproc_bold",
                  "space-template_res-derivative_desc-preproc_bold",
+                 "movement-parameters",
                  "regressors",
                  "FSL-AFNI-brain-mask",
                  "framewise-displacement-jenkinson",

CPAC/nuisance/nuisance.py

@@ -1,19 +1,19 @@
-"""Copyright (C) 2022  C-PAC Developers
+# Copyright (C) 2012-2023  C-PAC Developers
 
-This file is part of C-PAC.
+# This file is part of C-PAC.
 
-C-PAC is free software: you can redistribute it and/or modify it under
-the terms of the GNU Lesser General Public License as published by the
-Free Software Foundation, either version 3 of the License, or (at your
-option) any later version.
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
 
-C-PAC is distributed in the hope that it will be useful, but WITHOUT
-ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-License for more details.
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
 
-You should have received a copy of the GNU Lesser General Public
-License along with C-PAC. If not, see <https://www.gnu.org/licenses/>."""
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 import os
 import sys
 import time
@@ -42,7 +42,6 @@
 from CPAC.pipeline.engine import NodeBlock, initiate_rpool
 from CPAC.anat_preproc.anat_preproc import (
     freesurfer_reconall,
-    freesurfer_postproc,
     freesurfer_abcd_preproc,
     anatomical_init,
     acpc_align_head,
@@ -82,7 +81,7 @@
     brain_mask_T2,
     brain_mask_acpc_T2,
     brain_extraction_temp_T2,
-    brain_extraction_T2
+    brain_extraction_T2,
 )
 
 from CPAC.registration.registration import (
@@ -867,40 +866,28 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
         ]
         pipeline_blocks += anat_init_blocks
 
-    if rpool.check_rpool('freesurfer-subject-dir'):
-        pipeline_blocks += [freesurfer_postproc]
-    else:
+    if not rpool.check_rpool('freesurfer-subject-dir'):
         pipeline_blocks += [freesurfer_reconall]  # includes postproc
 
     if not rpool.check_rpool('desc-preproc_T1w'):
 
         # brain masking for ACPC alignment
         if cfg.anatomical_preproc['acpc_alignment']['acpc_target'] == 'brain':
-            if rpool.check_rpool('space-T1w_desc-brain_mask') or \
-                    cfg.surface_analysis['freesurfer']['run_reconall']:
-                acpc_blocks = [
-                    brain_extraction_temp,
-                    acpc_align_brain_with_mask
-                    # outputs space-T1w_desc-brain_mask for later - keep the mask (the user provided)
-                ]
-                acpc_blocks.append(
-                    [brain_mask_acpc_freesurfer_fsl_tight,
-                     brain_mask_acpc_freesurfer_fsl_loose]
-                )
-            else:
                 acpc_blocks = [
                     [brain_mask_acpc_afni,
                      brain_mask_acpc_fsl,
                      brain_mask_acpc_niworkflows_ants,
                      brain_mask_acpc_unet,
-                     brain_mask_acpc_freesurfer_abcd],
-                    #  brain_mask_acpc_freesurfer
-                    # we don't want these masks to be used later
+                     brain_mask_acpc_freesurfer_abcd,
+                     brain_mask_acpc,
+                     brain_mask_acpc_freesurfer,
+                     brain_mask_acpc_freesurfer_fsl_tight,
+                     brain_mask_acpc_freesurfer_fsl_loose],
+                    acpc_align_brain_with_mask,
                     brain_extraction_temp,
                     acpc_align_brain
                 ]
-        elif cfg.anatomical_preproc['acpc_alignment'][
-            'acpc_target'] == 'whole-head':
+        elif cfg.anatomical_preproc['acpc_alignment']['acpc_target'] == 'whole-head':
             if (rpool.check_rpool('space-T1w_desc-brain_mask') and \
                 cfg.anatomical_preproc['acpc_alignment']['align_brain_mask']) or \
                     cfg.surface_analysis['freesurfer']['run_reconall']:
@@ -912,6 +899,7 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
                 acpc_blocks = [
                     acpc_align_head  # does not output nor generate a mask
                 ]
+        
 
         anat_preproc_blocks = [
             (non_local_means, ('T1w', ['desc-preproc_T1w',
@@ -929,18 +917,18 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
         pipeline_blocks += [freesurfer_abcd_preproc]
 
     # Anatomical T1 brain masking
-    if not rpool.check_rpool('space-T1w_desc-brain_mask') or \
-        cfg.surface_analysis['freesurfer']['run_reconall']:
-        anat_brain_mask_blocks = [
-            [brain_mask_afni,
-             brain_mask_fsl,
-             brain_mask_niworkflows_ants,
-             brain_mask_unet,
-             brain_mask_freesurfer_abcd,
-             brain_mask_freesurfer_fsl_tight,
-             brain_mask_freesurfer_fsl_loose]
-        ]
-        pipeline_blocks += anat_brain_mask_blocks
+
+    anat_brain_mask_blocks = [
+        [brain_mask_afni,
+        brain_mask_fsl,
+        brain_mask_niworkflows_ants,
+        brain_mask_unet,
+        brain_mask_freesurfer_abcd,
+        brain_mask_freesurfer,
+        brain_mask_freesurfer_fsl_tight,
+        brain_mask_freesurfer_fsl_loose]
+    ]
+    pipeline_blocks += anat_brain_mask_blocks
 
     # T2w Anatomical Preprocessing
     if rpool.check_rpool('T2w'):
@@ -1032,7 +1020,6 @@ def build_T1w_registration_stack(rpool, cfg, pipeline_blocks=None):
             warp_T1mask_to_template
         ]
 
-
     if not rpool.check_rpool('desc-restore-brain_T1w'):
         reg_blocks.append(correct_restore_brain_intensity_abcd)
 
@@ -1363,6 +1350,7 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
 	    apply_func_warp['EPI'] = (_r_w_f_r['coregistration']['run'] and _r_w_f_r['func_registration_to_template']['run_EPI'])
     else:
         apply_func_warp['EPI'] = (_r_w_f_r['func_registration_to_template']['run_EPI'])
+    
     del _r_w_f_r
 
     template_funcs = [
@@ -1394,6 +1382,7 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
 
     # PostFreeSurfer and fMRISurface
     if not rpool.check_rpool('space-fsLR_den-32k_bold.dtseries'):
+        
         pipeline_blocks += [surface_postproc]
 
     # Extractions and Derivatives