Merge pull request #1932 from FCP-INDI/bugfix/log_subprocess

🐛 log_subprocess added as local import in function node

Author: sgiavasis

CHANGELOG.md

@@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added the ability to ingress FreeSurfer data into CPAC
 - Added the ability to toggle FreeSurfer derived masks for brain extraction
 - Added an optional volume center to FD-J calculation
+- Added new preconfig `abcd-prep`, which performs minimal preprocessing on the T1w data in preparation for Freesurfer Recon-All
 
 ### Changed
 - Freesurfer output directory ingress moved to the data configuration YAML

CPAC/anat_preproc/anat_preproc.py

@@ -16,7 +16,8 @@
     mri_convert, \
     wb_command, \
     fslmaths_command, \
-    VolumeRemoveIslands
+    VolumeRemoveIslands, \
+    normalize_wmparc
 from CPAC.pipeline.engine import flatten_list
 from CPAC.utils.docs import docstring_parameter
 from CPAC.utils.interfaces.fsl import Merge as fslMerge
@@ -925,23 +926,24 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     # Register wmparc file if ingressing FreeSurfer data
     if strat_pool.check_rpool('pipeline-fs_xfm'):
 
-        wmparc_to_native = pe.Node(
-            interface=freesurfer.ApplyVolTransform(),
-            name='wmparc_to_native')
+        wmparc_to_native = pe.Node(util.Function(input_names=['source_file',
+                                                            'target_file',
+                                                            'xfm',
+                                                            'out_file'],
+                                                output_names=['transformed_file'],
+                                                function=normalize_wmparc),
+                                        name=f'wmparc_to_native_{pipe_num}')
 
-        wmparc_to_native.inputs.reg_header = True
+        wmparc_to_native.inputs.out_file = 'wmparc_warped.mgz'
 
-        node, out = strat_pool.get_data('pipeline-fs_wmparc') 
+        node, out = strat_pool.get_data('pipeline-fs_wmparc')
         wf.connect(node, out, wmparc_to_native, 'source_file')
 
         node, out = strat_pool.get_data('pipeline-fs_raw-average')
         wf.connect(node, out, wmparc_to_native, 'target_file')
 
         node, out = strat_pool.get_data('pipeline-fs_xfm')
-        wf.connect(node, out, wmparc_to_native, 'xfm_reg_file')
-
-        node, out = strat_pool.get_data('freesurfer-subject-dir')
-        wf.connect(node, out, wmparc_to_native, 'subjects_dir')
+        wf.connect(node, out, wmparc_to_native, 'xfm')
 
         wf.connect(wmparc_to_native, 'transformed_file', wmparc_to_nifti, 'in_file')
 
@@ -1271,8 +1273,8 @@ def acpc_align_head(wf, cfg, strat_pool, pipe_num, opt=None):
                 ["anatomical_preproc", "run"]],
      "option_key": "None",
      "option_val": "None",
-     "inputs": ["desc-head_T1w",
-                "desc-preproc_T1w",
+     "inputs": [["desc-preproc_T1w",
+                "desc-head_T1w"],
                 "T1w-ACPC-template"],
      "outputs": ["desc-head_T1w",
                  "desc-preproc_T1w",
@@ -1285,7 +1287,7 @@ def acpc_align_head(wf, cfg, strat_pool, pipe_num, opt=None):
                                 mask=False,
                                 wf_name=f'acpc_align_{pipe_num}')
 
-    node, out = strat_pool.get_data(['desc-head_T1w', 'desc-preproc_T1w'])
+    node, out = strat_pool.get_data(['desc-preproc_T1w','desc-head_T1w'])
     wf.connect(node, out, acpc_align, 'inputspec.anat_leaf')
 
     node, out = strat_pool.get_data('T1w-ACPC-template')
@@ -2564,10 +2566,10 @@ def brain_extraction_temp_T2(wf, cfg, strat_pool, pipe_num, opt=None):
 def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     {"name": "freesurfer_abcd_preproc",
-     "config": ["anatomical_preproc", "brain_extraction"],
-     "switch": "None",
-     "option_key": "using",
-     "option_val": "FreeSurfer-ABCD",
+     "config": ["surface_analysis", "abcd_prefreesurfer_prep"],
+     "switch": ["run"],
+     "option_key": "None",
+     "option_val": "None",
      "inputs": ["desc-preproc_T1w",
                 "T1w-template",
                 "T1w-brain-template-mask",
@@ -2576,16 +2578,17 @@ def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
                 "freesurfer-subject-dir"],
      "outputs": ["desc-restore_T1w",
                  "desc-restore-brain_T1w",
+                 "desc-ABCDpreproc_T1w",
                  "pipeline-fs_desc-fast_biasfield",
                  "pipeline-fs_hemi-L_desc-surface_curv",
-                 "pipeline-fs_hemi-R_desc-surface_curv", 
+                 "pipeline-fs_hemi-R_desc-surface_curv",
                  "pipeline-fs_hemi-L_desc-surfaceMesh_pial",
                  "pipeline-fs_hemi-R_desc-surfaceMesh_pial",
                  "pipeline-fs_hemi-L_desc-surfaceMesh_smoothwm",
                  "pipeline-fs_hemi-R_desc-surfaceMesh_smoothwm",
                  "pipeline-fs_hemi-L_desc-surfaceMesh_sphere",
                  "pipeline-fs_hemi-R_desc-surfaceMesh_sphere",
-                 "pipeline-fs_hemi-L_desc-surfaceMap_sulc", 
+                 "pipeline-fs_hemi-L_desc-surfaceMap_sulc",
                  "pipeline-fs_hemi-R_desc-surfaceMap_sulc",
                  "pipeline-fs_hemi-L_desc-surfaceMap_thickness",
                  "pipeline-fs_hemi-R_desc-surfaceMap_thickness",
@@ -2691,7 +2694,9 @@ def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
             'desc-restore_T1w': (fast_correction, 'outputspec.anat_restore'),
             'desc-restore-brain_T1w': (fast_correction,
                                        'outputspec.anat_brain_restore'),
-            'pipeline-fs_desc-fast_biasfield': (fast_correction, 'outputspec.bias_field')}
+            'pipeline-fs_desc-fast_biasfield': (fast_correction, 'outputspec.bias_field'),
+            'desc-ABCDpreproc_T1w': (normalize_head, 'out_file')
+            }
     return (wf, outputs)
 
 # we're grabbing the postproc outputs and appending them to
@@ -2706,7 +2711,8 @@ def freesurfer_reconall(wf, cfg, strat_pool, pipe_num, opt=None):
       "switch": ["run_reconall"],
       "option_key": "None",
       "option_val": "None",
-      "inputs": ["desc-preproc_T1w"],
+      "inputs": [["desc-ABCDpreproc_T1w",
+                 "desc-preproc_T1w"]],
       "outputs": ["freesurfer-subject-dir",
                   "pipeline-fs_raw-average",
                   "pipeline-fs_subcortical-seg",
@@ -2739,7 +2745,7 @@ def freesurfer_reconall(wf, cfg, strat_pool, pipe_num, opt=None):
         reconall.inputs.args = cfg.surface_analysis['freesurfer'][
             'reconall_args']
 
-    node, out = strat_pool.get_data("desc-preproc_T1w")
+    node, out = strat_pool.get_data(["desc-ABCDpreproc_T1w","desc-preproc_T1w"])
     wf.connect(node, out, reconall, 'T1_files')
 
     wf, hemisphere_outputs = freesurfer_hemispheres(wf, reconall, pipe_num)
@@ -2974,9 +2980,9 @@ def fast_bias_field_correction(config=None, wf_name='fast_bias_field_correction'
 def correct_restore_brain_intensity_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     {"name": "correct_restore_brain_intensity_abcd",
-     "config": ["anatomical_preproc", "brain_extraction"],
-     "switch": "None",
-     "option_key": "using",
+     "config": "None",
+     "switch": ["anatomical_preproc", "brain_extraction", "run"],
+     "option_key": ["anatomical_preproc", "brain_extraction", "using"],
      "option_val": "FreeSurfer-ABCD",
      "inputs": [("desc-preproc_T1w",
                  "desc-n4_T1w",

CPAC/anat_preproc/utils.py

@@ -420,6 +420,15 @@ def fslmaths_command(in_file, number, out_file_suffix):
 
     return out_file
 
+def normalize_wmparc(source_file, target_file, xfm, out_file):
+    from CPAC.utils.monitoring.custom_logging import log_subprocess
+    import os
+
+    cmd = ['mri_vol2vol', '--mov', source_file, \
+                '--targ', target_file, '--o', out_file, '--lta', xfm]
+    log_subprocess(cmd)
+    output = os.path.join(os.getcwd(), out_file)
+    return output
 
 """This module provides interfaces for workbench -volume-remove-islands commands"""
 from nipype.interfaces.base import TraitedSpec, File, traits, CommandLineInputSpec

CPAC/pipeline/cpac_pipeline.py

@@ -864,8 +864,10 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
             anatomical_init
         ]
         pipeline_blocks += anat_init_blocks
+        
+    using_brain_extraction = cfg.anatomical_preproc['brain_extraction']['using']
 
-    if not rpool.check_rpool('freesurfer-subject-dir'):
+    if not rpool.check_rpool('freesurfer-subject-dir') and 'FreeSurfer-ABCD' not in using_brain_extraction:
         pipeline_blocks += [freesurfer_reconall]  # includes postproc
 
     if not rpool.check_rpool('desc-preproc_T1w'):
@@ -913,6 +915,9 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
 
         pipeline_blocks += [freesurfer_abcd_preproc]
 
+    if not rpool.check_rpool('freesurfer-subject-dir') and 'FreeSurfer-ABCD' in using_brain_extraction:
+        pipeline_blocks += [freesurfer_reconall]  # includes postproc
+
     # Anatomical T1 brain masking
 
     anat_brain_mask_blocks = [

CPAC/pipeline/engine.py

@@ -1723,7 +1723,7 @@ def ingress_raw_anat_data(wf, rpool, cfg, data_paths, unique_id, part_id,
             'pipeline-fs_hemi-R_desc-surfaceMap_volume': 'surf/rh.volume',
             'pipeline-fs_hemi-L_desc-surfaceMesh_white': 'surf/lh.white',
             'pipeline-fs_hemi-R_desc-surfaceMesh_white': 'surf/rh.white',
-            'pipeline-fs_xfm': 'mri/transforms/talairach.xfm'
+            'pipeline-fs_xfm': 'mri/transforms/talairach.lta'
         }
 
         for key, outfile in recon_outs.items():

CPAC/pipeline/schema.py

@@ -711,6 +711,9 @@ def sanitize(filename):
         },
     },
     'surface_analysis': {
+        'abcd_prefreesurfer_prep':{
+            'run': bool1_1,
+        },
         'freesurfer': {
             'run_reconall': bool1_1,
             'reconall_args': Maybe(str),

CPAC/registration/registration.py

@@ -4547,7 +4547,7 @@ def warp_bold_mask_to_T1template(wf, cfg, strat_pool, pipe_num, opt=None):
      "option_key": ["registration_workflows", "functional_registration",
                     "func_registration_to_template", "apply_transform",
                     "using"],
-     "option_val": ["default", "abcd", "dcan_nhp"],
+     "option_val": ["default"],
      "inputs": [("space-bold_desc-brain_mask",
                  "from-bold_to-template_mode-image_xfm"),
                 "T1w-brain-template-funcreg"],

CPAC/resources/configs/pipeline_config_abcd-options.yml

@@ -28,6 +28,10 @@ pipeline_setup:
 # -------------
 surface_analysis:
 
+  # Run freesurfer_abcd_preproc to obtain preprocessed T1w for reconall
+  abcd_prefreesurfer_prep:
+    run: On
+
   # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
   # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
   # select those 'Freesurfer-' labeled options further below in anatomical_preproc.