Merge remote-tracking branch 'origin/develop' into nuisance-CSF-LV

merging develop branch to update this branch from when it was created

Author: Amy Gutierrez

CHANGELOG.md

@@ -5,6 +5,34 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.8.3] - 2022-02-10
+
+### Added
+- Added XCP-style quality control file
+- Added RBC-options pipeline preconfiguration
+- Added `engine.log` (when verbose debugging is on)
+- Added ability to fix random seed for
+    - `antsAI`
+    - `antsRegistration`
+    - `Atropos` (fixed but not specified)
+    - `fslmaths`
+    - `mri_vol2vol`
+    - `recon-all`
+
+### Changed
+- In a given pipeline configuration, segmentation probability maps and binary tissue masks are warped to template space, and those warped masks are included in the output directory
+    - if `registration_workflows['functional_registration']['EPI_registration']['run segmentation']` is `On` and `segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation']` includes `EPI_Template`
+    
+      and/or
+    - if `registration_workflows['anatomical_registration']['run']` is `On` and `segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation']` includes `T1_Template`
+- Renamed connectivity matrices from `*_connectome.tsv` to `*_correlations.tsv`
+- Moved some ephemeral logging statements into `pypeline.log`
+
+### Fixed
+- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1638) in which working connectivity matrix filepaths were generated incorrectly, preventing generating matrices depending on container bindings
+- Fixed broken links in README
+- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1575) in which anatomical-only configurations required functional data directories
+
 ## [1.8.2] - 2021-12-02
 
 ### Added 
@@ -41,5 +69,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 See [Version 1.8.1 Beta](https://fcp-indi.github.io/docs/user/release_notes/v1.8.1) for release notes for v1.8.1 and [Release Notes](https://fcp-indi.github.io/docs/user/release_notes) for all release notes back to v0.1.1.
 
-[unreleased]: https://github.com/FCP-INDI/C-PAC/compare/v1.8.1...develop
+[1.8.3]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.3
+[1.8.2]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.2
 [1.8.1]: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.8.1

CPAC/anat_preproc/anat_preproc.py

@@ -687,22 +687,19 @@ def fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
 
 def niworkflows_ants_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     # Skull-stripping using niworkflows-ants
-    anat_skullstrip_ants = init_brain_extraction_wf(tpl_target_path=
-                                                    cfg.anatomical_preproc[
-                                                        'brain_extraction'][
-                                                        'niworkflows-ants'][
-                                                        'template_path'],
-                                                    tpl_mask_path=
-                                                    cfg.anatomical_preproc[
-                                                        'brain_extraction'][
-                                                        'niworkflows-ants'][
-                                                        'mask_path'],
-                                                    tpl_regmask_path=
-                                                    cfg.anatomical_preproc[
-                                                        'brain_extraction'][
-                                                        'niworkflows-ants'][
-                                                        'regmask_path'],
-                                                    name='anat_skullstrip_ants')
+    anat_skullstrip_ants = init_brain_extraction_wf(
+        tpl_target_path=cfg.anatomical_preproc['brain_extraction'][
+                                               'niworkflows-ants'][
+                                               'template_path'],
+        tpl_mask_path=cfg.anatomical_preproc['brain_extraction'][
+                                             'niworkflows-ants'][
+                                             'mask_path'],
+        tpl_regmask_path=cfg.anatomical_preproc['brain_extraction'][
+                                                'niworkflows-ants'][
+                                                'regmask_path'],
+        name='anat_skullstrip_ants',
+        atropos_use_random_seed=cfg.pipeline_setup['system_config'][
+            'random_seed'] is None)
 
     if strat_pool.check_rpool('desc-preproc_T1w') or \
         strat_pool.check_rpool('desc-reorient_T1w') or \
@@ -3191,7 +3188,7 @@ def correct_restore_brain_intensity_abcd(wf, cfg, strat_pool, pipe_num, opt=None
     wf.connect(node, out, merge_t1_acpc_to_list, 'in3')
 
     merge_t1_acpc = pe.Node(interface=fslMerge(),
-                            name='merge_t1_acpc')
+                            name=f'merge_t1_acpc_{pipe_num}')
 
     merge_t1_acpc.inputs.dimension = 't'
 

CPAC/anat_preproc/ants.py

@@ -12,7 +12,7 @@
 
 # general purpose
 from collections import OrderedDict
-from multiprocessing import cpu_count
+from logging import getLogger
 from pkg_resources import resource_filename as pkgr_fn
 from packaging.version import parse as parseversion, Version
 
@@ -440,6 +440,9 @@ def init_atropos_wf(name='atropos_wf',
         use_random_seed=use_random_seed),
         name='01_atropos', n_procs=omp_nthreads, mem_gb=mem_gb)
 
+    if not use_random_seed:
+        getLogger('random').info('%s  # (Atropos constant)', atropos.name)
+
     # massage outputs
     pad_segm = pe.Node(ImageMath(operation='PadImage', op2='%d' % padding),
                        name='02_pad_segm')

CPAC/connectome/connectivity_matrix.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """Functions for creating connectome connectivity matrices."""
+import os
 from warnings import warn
 import numpy as np
 from nilearn.connectome import ConnectivityMeasure
@@ -20,13 +21,11 @@
 }
 
 
-def connectome_name(timeseries, atlas_name, tool, method):
+def connectome_name(atlas_name, tool, method):
     """Helper function to create connectome file filename
 
     Parameters
     ----------
-    timeseries : str
-        path to input timeseries
 
     atlas_name : str
         atlas name
@@ -41,19 +40,9 @@ def connectome_name(timeseries, atlas_name, tool, method):
     -------
     str
     """
-    method = ''.join(word.capitalize() for word in [tool, method])
-    new_filename_parts = [part for part in timeseries.split('_')[:-1][::-1] if
-                          not part.startswith('space-')]
-    atlas_index = len(new_filename_parts) - 1
-    if any(filename_part.startswith('desc-') for filename_part in
-            new_filename_parts):
-        for i, filename_part in enumerate(new_filename_parts):
-            if filename_part.startswith('desc-'):
-                new_filename_parts[-i] = f'desc-{method}'
-                atlas_index = -(i - 1)
-                break
-    new_filename_parts.insert(atlas_index, f'atlas-{atlas_name}')
-    return '_'.join([*new_filename_parts[::-1], 'connectome.tsv'])
+    return os.path.join(os.getcwd(), '_'.join([
+        f'atlas-{atlas_name}', f'desc-{tool}{method}', 'connectome.tsv'
+    ]))
 
 
 def get_connectome_method(method, tool):
@@ -111,7 +100,7 @@ def compute_connectome_nilearn(in_rois, in_file, method, atlas_name):
     numpy.ndarray or NotImplemented
     """
     tool = 'Nilearn'
-    output = connectome_name(in_file, atlas_name, tool, method)
+    output = connectome_name(atlas_name, tool, method)
     method = get_connectome_method(method, tool)
     if method is NotImplemented:
         return NotImplemented
@@ -156,21 +145,21 @@ def create_connectome_afni(name, method, pipe_num):
                                 name='netcorrStripHeader'
                                      f'{method}_{pipe_num}')
 
-    name_output_node = pe.Node(Function(input_names=['timeseries',
-                                                     'atlas_name',
+    name_output_node = pe.Node(Function(input_names=['atlas_name',
                                                      'tool',
                                                      'method'],
                                         output_names=['filename'],
+                                        imports=['import os'],
                                         function=connectome_name),
-                               name=f'connectomeName{method}_{pipe_num}')
+                               name=f'connectomeName{method}_{pipe_num}',
+                               as_module=True)
     name_output_node.inputs.tool = 'Afni'
 
     wf.connect([
         (inputspec, timeseries_correlation, [('in_rois', 'in_rois'),
                                              ('in_file', 'in_file'),
                                              ('mask', 'mask')]),
-        (inputspec, name_output_node, [('in_file', 'timeseries'),
-                                       ('atlas_name', 'atlas_name'),
+        (inputspec, name_output_node, [('atlas_name', 'atlas_name'),
                                        ('method', 'method')]),
         (timeseries_correlation, strip_header_node, [
             ('out_corr_matrix', 'in_file')]),

CPAC/cwas/tests/test_cwas.py

@@ -78,7 +78,8 @@ def run_cwas(self):
 
         # Read in list of subject functionals
         subjects_list = [
-            l.strip().strip('"') for l in open(sfile).readlines()  # noqa E741
+            l.strip().strip('"') for  # noqa: E741
+            l in open(sfile).readlines()  # pylint: disable=consider-using-with
         ]
 
         # Read in design/regressor file
@@ -93,7 +94,7 @@ def run_cwas(self):
         c.inputs.inputspec.f_samples = nperms
         c.inputs.inputspec.parallel_nodes = 4
         # c.base_dir = op.join(obase, 'results_fs%i_pn%i' % \
-        #                (c.inputs.inputspec.f_samples, c.inputs.inputspec.parallel_nodes))  # noqa E501
+        #                (c.inputs.inputspec.f_samples, c.inputs.inputspec.parallel_nodes))  # noqa: E501  # pylint: disable=line-too-long
         c.base_dir = op.join(self.base, "results_%s.py" % self.name)
 
         # export MKL_NUM_THREADS=X # in command line

CPAC/func_preproc/func_ingress.py

@@ -1,5 +1,5 @@
 from nipype import logging
-logger = logging.getLogger('workflow')
+logger = logging.getLogger('nipype.workflow')
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
 

CPAC/func_preproc/func_preproc.py

@@ -1,7 +1,7 @@
 from nipype import logging
 from nipype.interfaces import ants
 
-logger = logging.getLogger('workflow')
+logger = logging.getLogger('nipype.workflow')
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.fsl as fsl

CPAC/info.py

@@ -10,7 +10,7 @@
 # version
 _version_major = 1
 _version_minor = 8
-_version_micro = 2
+_version_micro = 3
 _version_extra = ''
 
 
@@ -87,15 +87,15 @@ def get_cpac_gitversion():
 Website
 -------
 
-CPAC website is located here:  http://fcp-indi.github.com/
+CPAC website is located here:  https://fcp-indi.github.io/
 
 
 Documentation
 -------------
 
-User documentation can be found here: http://fcp-indi.github.com/docs/user/index.html
+User documentation can be found here: https://fcp-indi.github.io/docs/user/index.html
 
-Developer documention can be found here: http://fcp-indi.github.com/docs/developer/index.html
+Developer documention can be found here: https://fcp-indi.github.io/docs/developer/index.html
 
 Documentation pertaining to this latest release can be found here: https://github.com/FCP-INDI/C-PAC/releases/tag/v1.3.0
 
@@ -161,6 +161,5 @@ def get_cpac_gitversion():
     "simplejson==3.15.0",
     "traits==4.6.0",
     "PyBASC==0.4.5",
-    "pathlib==1.0.1",
     "voluptuous>=0.12.0",
 ]

CPAC/network_centrality/pipeline.py

@@ -9,7 +9,7 @@
 from CPAC.network_centrality.utils import merge_lists, check_centrality_params
 from CPAC.pipeline.schema import valid_options
 
-logger = logging.getLogger('workflow')
+logger = logging.getLogger('nipype.workflow')
 
 
 def connect_centrality_workflow(workflow, c, resample_functional_to_template,