🔀 Merge v1.8.3 to main (#1658)

Author: shnizzedy

CHANGELOG.md

@@ -5,6 +5,36 @@ 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] - 2022-02-11
+
+### 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`
+- Added ability to use lateral ventricles mask in place of cerebrospinal fluid mask when when segmentation is Off, specifically for the rodent pipeline, but works on any dataset when segmentation is off
+
+### 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
+- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1532) in which nuisance regressors would crash when segmentation is off and no CSF mask is provided
+
 ## [1.8.2] - 2021-12-02
 
 ### Added 
@@ -41,5 +71,6 @@ 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,