🎨 Standardize naming for atlases used in RBC

CPAC/pipeline/engine.py

@@ -1785,12 +1785,12 @@ def ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path=None):
             val = val.replace('${func_resolution}', cfg.registration_workflows[
                 'functional_registration']['func_registration_to_template'][
                 'output_resolution'][tag])
-            
+
         if desc:
-            template_name = lookup_identifier(val)
+            template_name, _template_desc = lookup_identifier(val)
             if template_name:
                 desc = f"{template_name} - {desc}"
-            json_info['Description'] = f"{desc} - {val}"     
+            json_info['Description'] = f"{desc} - {val}"
         if resolution:
             resolution = cfg.get_nested(cfg, res_keys)
             json_info['Resolution'] = resolution

CPAC/pipeline/schema.py

@@ -23,7 +23,7 @@
 from pathvalidate import sanitize_filename
 from voluptuous import All, ALLOW_EXTRA, Any, Capitalize, Coerce, \
                        ExactSequence, ExclusiveInvalid, In, Length, Lower, \
-                       Match, Maybe, Optional, Range, Required, Schema
+                       Match, Maybe, Optional, Range, Required, Schema, Title
 from CPAC import docs_prefix
 from CPAC.utils.datatypes import ListFromItem
 from CPAC.utils.utils import YAML_BOOLS
@@ -204,6 +204,8 @@ def str_to_bool1_1(x):  # pylint: disable=invalid-name
         },
     }, dict  # TODO: specify other valid ANTs parameters
 )]
+target_space = All(Coerce(ListFromItem),
+                   [All(Title, In(valid_options['target_space']))])
 
 
 def permutation_message(key, options):
@@ -865,7 +867,7 @@ def sanitize(filename):
     },
     'amplitude_low_frequency_fluctuation': {
         'run': bool1_1,
-        'target_space': [In(valid_options['target_space'])],
+        'target_space': target_space,
         'highpass_cutoff': [float],
         'lowpass_cutoff': [float],
     },
@@ -884,7 +886,7 @@ def sanitize(filename):
     },
     'regional_homogeneity': {
         'run': bool1_1,
-        'target_space': [In(valid_options['target_space'])],
+        'target_space': target_space,
         'cluster_size': In({7, 19, 27}),
     },
     'post_processing': {

CPAC/resources/configs/pipeline_config_rbc-options.yml

@@ -118,6 +118,10 @@ functional_preproc:
 nuisance_corrections:
   2-nuisance_regression:
 
+    # this is a fork point
+    #   run: [On, Off] - this will run both and fork the pipeline
+    run: [On]
+
     # Select which nuisance signal corrections to apply
     Regressors:
       - Name: 36-parameter
@@ -230,12 +234,18 @@ amplitude_low_frequency_fluctuation:
   # Calculate Amplitude of Low Frequency Fluctuations (ALFF) and fractional ALFF (f/ALFF) for all voxels.
   run: On
 
+  # space: Template or Native
+  target_space: [Template]
+
 regional_homogeneity:
 
   # ReHo
   # Calculate Regional Homogeneity (ReHo) for all voxels.
   run: On
 
+  # space: Template or Native
+  target_space: [Template]
+
 network_centrality:
 
   # Calculate Degree, Eigenvector Centrality, or Functional Connectivity Density.

CPAC/resources/templates/BIDS_identifiers.tsv

@@ -1,13 +1,30 @@
-/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_T1w_reference.nii.gz	MNI152NLin2009cAsym
-/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_desc-brain_T1w.nii.gz	MNI152NLin2009cAsym
-/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_desc-brain_mask.nii.gz	MNI152NLin2009cAsym
-/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_desc-fMRIPrep_boldref.nii.gz	MNI152NLin2009cAsym
-/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_label-brain_probseg.nii.gz	MNI152NLin2009cAsym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*.nii.gz	MNI152NLin6ASym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain.nii.gz	MNI152NLin6ASym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask.nii.gz	MNI152NLin6ASym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask_dil.nii.gz	MNI152NLin6ASym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_symmetric.nii.gz	MNI152NLin6Sym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_symmetric.nii.gz	MNI152NLin6Sym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask_symmetric.nii.gz	MNI152NLin6Sym
-/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask_symmetric_dil.nii.gz	MNI152NLin6Sym
+/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_T1w_reference.nii.gz	MNI152NLin2009cAsym	
+/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_desc-brain_T1w.nii.gz	MNI152NLin2009cAsym	
+/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_desc-brain_mask.nii.gz	MNI152NLin2009cAsym	
+/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_desc-fMRIPrep_boldref.nii.gz	MNI152NLin2009cAsym	
+/code/CPAC/resources/templates/tpl-MNI152NLin2009cAsym_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_label-brain_probseg.nii.gz	MNI152NLin2009cAsym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*.nii.gz	MNI152NLin6ASym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain.nii.gz	MNI152NLin6ASym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask.nii.gz	MNI152NLin6ASym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask_dil.nii.gz	MNI152NLin6ASym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_symmetric.nii.gz	MNI152NLin6Sym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_symmetric.nii.gz	MNI152NLin6Sym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask_symmetric.nii.gz	MNI152NLin6Sym	
+/usr/share/fsl/5.0/data/standard/MNI152_T1_(res-){0,1}[0-9]+(\.[0-9]*){0,1}[a-z]*(x[0-9]+(\.[0-9]*){0,1}[a-z]*)*_brain_mask_symmetric_dil.nii.gz	MNI152NLin6Sym	
+/ndmg_atlases/label/Human/AAL_space-MNI152NLin6_res-2x2x2.nii.gz	AAL	
+/ndmg_atlases/label/Human/Brodmann_space-MNI152NLin6_res-2x2x2.nii.gz	Brodmann	
+/cpac_templates/CC200.nii.gz	CC	200
+/cpac_templates/CC400.nii.gz	CC	400
+/ndmg_atlases/label/Human/Glasser_space-MNI152NLin6_res-2x2x2.nii.gz	Glasser	
+/ndmg_atlases/label/Human/Slab907_space-MNI152NLin6_res-2x2x2.nii.gz	Slab	
+/ndmg_atlases/label/Human/HarvardOxfordcort-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz	HOCPA	th25
+/ndmg_atlases/label/Human/HarvardOxfordsub-maxprob-thr25_space-MNI152NLin6_res-2x2x2.nii.gz	HOSPA	th25
+/ndmg_atlases/label/Human/Juelich_space-MNI152NLin6_res-2x2x2.nii.gz	Juelich	
+/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-200Parcels17NetworksOrder.nii.gz	Schaefer2018	200p17n
+/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-300Parcels17NetworksOrder.nii.gz	Schaefer2018	300p17n
+/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-400Parcels17NetworksOrder.nii.gz	Schaefer2018	400p17n
+/cpac_templates/Schaefer2018_space-FSLMNI152_res-2mm_desc-1000Parcels17NetworksOrder.nii.gz	Schaefer2018	1000p17n
+/ndmg_atlases/label/Human/Yeo-7_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	7
+/ndmg_atlases/label/Human/Yeo-7-liberal_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	7liberal
+/ndmg_atlases/label/Human/Yeo-17_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	17
+/ndmg_atlases/label/Human/Yeo-17-liberal_space-MNI152NLin6_res-2x2x2.nii.gz	Yeo	17liberal

CPAC/resources/templates/__init__.py

@@ -1,4 +1,4 @@
 '''Template resources for C-PAC'''
-from .lookup_table import lookup_identifier
+from .lookup_table import format_identifier, lookup_identifier
 
-__all__ = ['lookup_identifier']
+__all__ = ['format_identifier', 'lookup_identifier']

CPAC/resources/templates/lookup_table.py

@@ -1,17 +1,58 @@
-'''Utilities for determining BIDS standard template identifiers
+# Copyright (C) 2022  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/>.
+"""Utilities for determining BIDS standard template identifiers
 (https://bids-specification.readthedocs.io/en/stable/99-appendices/08-coordinate-systems.html#standard-template-identifiers)
-from in-container template paths'''
-import os
-import re
-import numpy as np
+from in-container template paths"""
+from os import path as op
+from re import search
+from typing import Optional, Tuple
+from numpy import loadtxt
+
+LOOKUP_TABLE = {row[0]: (row[1], str(row[2]) if row[2] else None) for row in
+                loadtxt(op.join(op.dirname(__file__), 'BIDS_identifiers.tsv'),
+                        dtype='str', delimiter='\t')}
+
+
+def format_identifier(identifier: str, desc: Optional[str] = None) -> str:
+    '''Function to create an identifier string from a name and description
+
+    Parameters
+    ----------
+    identifier : str
+
+    desc : str, optional
+
+    Returns
+    -------
+    str
 
-LOOKUP_TABLE = {row[0]: row[1] for row in
-                np.loadtxt(os.path.join(os.path.dirname(__file__),
-                                        'BIDS_identifiers.tsv'),
-                dtype='str', delimiter='\t')}
+    Examples
+    --------
+    >>> format_identifier('CC', '200')
+    'CC_desc-200'
+    >>> format_identifier('AAL')
+    'AAL'
+    '''
+    if desc:
+        return f'{identifier}_desc-{desc}'
+    return identifier
 
 
-def lookup_identifier(template_path: str) -> str:
+def lookup_identifier(template_path: str) -> Tuple[str, None]:
     '''Function to return a standard template identifier for a packaged
     template, if known. Otherwise, returns the literal string
     'template'
@@ -24,19 +65,23 @@ def lookup_identifier(template_path: str) -> str:
     -------
     identifier : str
 
+    desc : str or None
+
     Examples
     --------
     >>> lookup_identifier('/usr/share/fsl/5.0/data/standard/'
     ...                   'MNI152_T1_1mm_brain.nii.gz')
-    'MNI152NLin6ASym'
+    ('MNI152NLin6ASym', None)
     >>> lookup_identifier('/code/CPAC/resources/templates/'
     ...                   'tpl-MNI152NLin2009cAsym_res-01_label-brain_'
     ...                   'probseg.nii.gz')
-    'MNI152NLin2009cAsym'
+    ('MNI152NLin2009cAsym', None)
     >>> lookup_identifier('/cpac_templates/chd8_functional_template_sk.nii')
-    'template'
+    ('template', None)
+    >>> lookup_identifier('/cpac_templates/CC200.nii.gz')
+    ('CC', '200')
     '''
     for key, value in LOOKUP_TABLE.items():
-        if re.search(key, template_path) is not None:
+        if search(key, template_path) is not None:
             return value
-    return 'template'
+    return 'template', None

CPAC/utils/datasource.py

@@ -17,11 +17,12 @@
 import csv
 import json
 import re
-from typing import Optional, Tuple
+from typing import Tuple
 from nipype import logging
 from nipype.interfaces import utility as util
-from nipype.interfaces.fsl import MultiImageMaths
 from CPAC.pipeline import nipype_pipeline_engine as pe
+from CPAC.resources.templates.lookup_table import format_identifier, \
+                                                  lookup_identifier
 from CPAC.utils import function
 from CPAC.utils.interfaces.function import Function
 from CPAC.utils.utils import get_scan_params
@@ -1016,33 +1017,36 @@ def create_roi_mask_dataflow(masks, wf_name='datasource_roi_mask'):
         if mask_file.strip() == '' or mask_file.startswith('#'):
             continue
 
-        base_file = os.path.basename(mask_file)
+        name, desc = lookup_identifier(mask_file)
 
-        try:
-            valid_extensions = ['.nii', '.nii.gz']
-
-            base_name = [
-                base_file[:-len(ext)]
-                for ext in valid_extensions
-                if base_file.endswith(ext)
-                ][0]
-
-            if base_name in mask_dict:
-                raise ValueError(
-                    'Files with same name not allowed: %s %s' % (
-                        mask_file,
-                        mask_dict[base_name]
-                    )
-                )
+        if name == 'template':
+            base_file = os.path.basename(mask_file)
 
-            mask_dict[base_name] = mask_file
+            try:
+                valid_extensions = ['.nii', '.nii.gz']
+
+                base_name = [
+                    base_file[:-len(ext)]
+                    for ext in valid_extensions
+                    if base_file.endswith(ext)
+                    ][0]
+
+            except IndexError:
+                # pylint: disable=raise-missing-from
+                raise ValueError('Error in spatial_map_dataflow: File '
+                                 f'extension of {base_file} not ".nii" or '
+                                 '.nii.gz')
+
+            except Exception as e:
+                raise e
+        else:
+            base_name = format_identifier(name, desc)
 
-        except IndexError as e:
-            raise Exception('Error in spatial_map_dataflow: '
-                            'File extension not in .nii and .nii.gz')
+        if base_name in mask_dict:
+            raise ValueError('Duplicate templates/atlases not allowed: '
+                             f'{mask_file} {mask_dict[base_name]}')
 
-        except Exception as e:
-            raise e
+        mask_dict[base_name] = mask_file
 
     wf = pe.Workflow(name=wf_name)
 

CPAC/utils/utils.py

@@ -182,7 +182,7 @@ def create_id_string(unique_id, resource, scan_id=None, template_desc=None,
     """
 
     if atlas_id:
-        if '_' in atlas_id:
+        if not (atlas_id.count('_') == 1 and '_desc-' in atlas_id):
             atlas_id = atlas_id.replace('_', '')
         resource = f'atlas-{atlas_id}_{resource}'