Merge branch 'develop' into art/DRY-convert_pedir

Author: sgiavasis

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### 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
 

CPAC/nuisance/nuisance.py

@@ -1758,7 +1758,7 @@ def ICA_AROMA_FSLreg(wf, cfg, strat_pool, pipe_num, opt=None):
      "inputs": [["desc-preproc_bold", "bold"],
                 "from-bold_to-T1w_mode-image_desc-linear_xfm",
                 "from-T1w_to-template_mode-image_xfm"],
-     "outputs": ["desc-preproc_bold", 
+     "outputs": ["desc-preproc_bold",
                  "desc-cleaned_bold"]}
     '''
 
@@ -1908,8 +1908,8 @@ def ICA_AROMA_FSLEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
     }
 
     return (wf, outputs)
-    
-    
+
+
 def ICA_AROMA_ANTsEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     Node Block:
@@ -1935,7 +1935,7 @@ def ICA_AROMA_ANTsEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
 
     if reg_tool != 'ants':
         return (wf, None)
-        
+
     num_cpus = cfg.pipeline_setup['system_config'][
         'max_cores_per_participant']
 
@@ -1972,7 +1972,7 @@ def ICA_AROMA_ANTsEPIreg(wf, cfg, strat_pool, pipe_num, opt=None):
 
     node, out = strat_pool.get_data('from-EPItemplate_to-bold_mode-image_xfm')
     wf.connect(node, out, apply_xfm, 'inputspec.transform')
-    
+
     outputs = {
         'desc-preproc_bold': (apply_xfm, 'outputspec.output_image'),
         'desc-cleaned_bold': (apply_xfm, 'outputspec.output_image')
@@ -2006,7 +2006,7 @@ def erode_mask_T1w(wf, cfg, strat_pool, pipe_num, opt=None):
 
     node, out = strat_pool.get_data('space-T1w_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
-    
+
     node, out = strat_pool.get_data(['label-CSF_desc-preproc_mask',
                                      'label-CSF_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
@@ -2121,15 +2121,15 @@ def erode_mask_WM(wf, cfg, strat_pool, pipe_num, opt=None):
     erode.inputs.inputspec.erode_prop = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_erosion_prop']
-        
+
     erode.inputs.inputspec.mask_erode_mm = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_mask_erosion_mm']
 
     node, out = strat_pool.get_data(['label-WM_desc-preproc_mask',
                                      'label-WM_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
-    
+
     node, out = strat_pool.get_data('space-T1w_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
 
@@ -2138,8 +2138,8 @@ def erode_mask_WM(wf, cfg, strat_pool, pipe_num, opt=None):
     }
 
     return (wf, outputs)
-    
-    
+
+
 def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     Node Block:
@@ -2174,7 +2174,7 @@ def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
             'from-template_to-T1w_mode-image_desc-linear_xfm')
         reg_tool = check_prov_for_regtool(xfm_prov)
         use_ants = reg_tool == 'ants'
-    
+
     ventricle = strat_pool.check_rpool('lateral-ventricles-mask')
 
     regressors = create_regressor_workflow(opt, use_ants,
@@ -2203,7 +2203,7 @@ def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
                                "label-CSF_desc-preproc_mask",
                                "label-CSF_mask"]):
         node, out = strat_pool.get_data(["label-CSF_desc-eroded_mask",
-                                         "label-CSF_desc-preproc_mask", 
+                                         "label-CSF_desc-preproc_mask",
                                          "label-CSF_mask"])
         wf.connect(node, out, regressors, 'inputspec.csf_mask_file_path')
 
@@ -2216,10 +2216,10 @@ def nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt=None):
         wf.connect(node, out, regressors, 'inputspec.wm_mask_file_path')
 
     if strat_pool.check_rpool(["label-GM_desc-eroded_mask",
-                               "label-GM_desc-preproc_mask", 
+                               "label-GM_desc-preproc_mask",
                                "label-GM_mask"]):
         node, out = strat_pool.get_data(["label-GM_desc-eroded_mask",
-                                         "label-GM_desc-preproc_mask", 
+                                         "label-GM_desc-preproc_mask",
                                          "label-GM_mask"])
         wf.connect(node, out, regressors, 'inputspec.gm_mask_file_path')
 
@@ -2359,7 +2359,7 @@ def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt=None):
 
         elif cfg.nuisance_corrections['2-nuisance_regression'][
             'bandpass_filtering_order'] == 'Before':
-            
+
             node, out = strat_pool.get_data("desc-preproc_bold")
             wf.connect(node, out, filt, 'inputspec.functional_file_path')
 
@@ -2409,7 +2409,7 @@ def erode_mask_bold(wf, cfg, strat_pool, pipe_num, opt=None):
 
     node, out = strat_pool.get_data('space-bold_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
-    
+
     node, out = strat_pool.get_data(['space-bold_label-CSF_desc-preproc_mask',
                                      'space-bold_label-CSF_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
@@ -2419,8 +2419,8 @@ def erode_mask_bold(wf, cfg, strat_pool, pipe_num, opt=None):
     }
 
     return (wf, outputs)
-    
-    
+
+
 def erode_mask_boldCSF(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     {"name": "erode_mask_boldCSF",
@@ -2524,15 +2524,15 @@ def erode_mask_boldWM(wf, cfg, strat_pool, pipe_num, opt=None):
     erode.inputs.inputspec.erode_prop = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_erosion_prop']
-        
+
     erode.inputs.inputspec.mask_erode_mm = cfg.nuisance_corrections[
         '2-nuisance_regression']['regressor_masks']['erode_wm'][
         'wm_mask_erosion_mm']
 
     node, out = strat_pool.get_data(['space-bold_label-WM_desc-preproc_mask',
                                      'space-bold_label-WM_mask'])
     wf.connect(node, out, erode, 'inputspec.mask')
-    
+
     node, out = strat_pool.get_data('space-bold_desc-brain_mask')
     wf.connect(node, out, erode, 'inputspec.brain_mask')
 
@@ -2559,7 +2559,7 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
                  "framewise-displacement-power",
                  "dvars",
                  ["space-bold_desc-eroded_mask", "space-bold_desc-brain_mask"],
-                 ["space-bold_label-CSF_desc-eroded_mask", "space-bold_label-CSF_desc-preproc_mask", 
+                 ["space-bold_label-CSF_desc-eroded_mask", "space-bold_label-CSF_desc-preproc_mask",
                   "space-bold_label-CSF_mask"],
                  ["space-bold_label-WM_desc-eroded_mask", "space-bold_label-WM_desc-preproc_mask",
                   "space-bold_label-WM_mask"],
@@ -2627,29 +2627,29 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
         wf.connect(node, out,
                    regressors, 'inputspec.lat_ventricles_mask_file_path')
 
-    if strat_pool.check_rpool('from-EPItemplate_to-bold_mode-image_desc-linear_xfm'):    
+    if strat_pool.check_rpool('from-EPItemplate_to-bold_mode-image_desc-linear_xfm'):
         node, out = strat_pool.get_data('from-EPItemplate_to-bold_mode-image_desc-linear_xfm')
         wf.connect(node, out, regressors, 'inputspec.mni_to_anat_linear_xfm_file_path')
         wf.connect(node, out, regressors, 'inputspec.anat_to_func_linear_xfm_file_path')
 
-    if strat_pool.check_rpool('from-bold_to-EPItemplate_mode-image_desc-linear_xfm'):    
+    if strat_pool.check_rpool('from-bold_to-EPItemplate_mode-image_desc-linear_xfm'):
         node, out = strat_pool.get_data('from-bold_to-EPItemplate_mode-image_desc-linear_xfm')
         wf.connect(node, out, regressors, 'inputspec.anat_to_mni_linear_xfm_file_path')
         wf.connect(node, out, regressors, 'inputspec.func_to_anat_linear_xfm_file_path')
 
-    if strat_pool.check_rpool('movement-parameters'):    
+    if strat_pool.check_rpool('movement-parameters'):
         node, out = strat_pool.get_data('movement-parameters')
         wf.connect(node, out, regressors, 'inputspec.motion_parameters_file_path')
 
-    if strat_pool.check_rpool('framewise-displacement-jenkinson'):    
+    if strat_pool.check_rpool('framewise-displacement-jenkinson'):
         node, out = strat_pool.get_data('framewise-displacement-jenkinson')
         wf.connect(node, out, regressors, 'inputspec.fd_j_file_path')
 
-    if strat_pool.check_rpool('framewise-displacement-power'):    
+    if strat_pool.check_rpool('framewise-displacement-power'):
         node, out = strat_pool.get_data('framewise-displacement-power')
         wf.connect(node, out, regressors, 'inputspec.fd_p_file_path')
 
-    if strat_pool.check_rpool('dvars'):    
+    if strat_pool.check_rpool('dvars'):
         node, out = strat_pool.get_data('dvars')
         wf.connect(node, out, regressors, 'inputspec.dvars_file_path')
 

CPAC/pipeline/cpac_pipeline.py

@@ -92,7 +92,11 @@
     warp_deriv_mask_to_EPItemplate,
     warp_timeseries_to_T1template_abcd,
     single_step_resample_timeseries_to_T1template,
+    warp_timeseries_to_T1template_dcan_nhp,
+    warp_Tissuemask_to_T1template,
+    warp_Tissuemask_to_EPItemplate,
     warp_timeseries_to_T1template_dcan_nhp
+
 )
 
 from CPAC.seg_preproc.seg_preproc import (
@@ -838,7 +842,7 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
                 ]
 
         anat_preproc_blocks = [
-            (non_local_means, ('T1w', ['desc-preproc_T1w', 
+            (non_local_means, ('T1w', ['desc-preproc_T1w',
                                        'desc-reorient_T1w',
                                        'T1w'])),
             n4_bias_correction
@@ -849,7 +853,7 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
             anat_blocks = anat_preproc_blocks + acpc_blocks
 
         pipeline_blocks += anat_blocks
-    
+
         if not rpool.check_rpool('freesurfer-subject-dir'):
             pipeline_blocks += [freesurfer_abcd_preproc]
 
@@ -868,14 +872,14 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
         pipeline_blocks += anat_brain_mask_blocks
 
     # T2w Anatomical Preprocessing
-    if rpool.check_rpool('T2w'): 
+    if rpool.check_rpool('T2w'):
         if not rpool.check_rpool('desc-reorient_T2w'):
             anat_init_blocks_T2 = [
-                anatomical_init_T2                    
+                anatomical_init_T2
             ]
             pipeline_blocks += anat_init_blocks_T2
-        
-        # TODO: T2 freesurfer_preproc? 
+
+        # TODO: T2 freesurfer_preproc?
         # pipeline_blocks += [freesurfer_preproc]
 
         if not rpool.check_rpool('desc-preproc_T2w'):
@@ -908,7 +912,7 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
                     ]
 
             anat_preproc_blocks_T2 = [
-                registration_T2w_to_T1w, 
+                registration_T2w_to_T1w,
                 non_local_means_T2,
                 n4_bias_correction_T2,
                 t1t2_bias_correction
@@ -919,7 +923,7 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
                 anat_blocks_T2 = anat_preproc_blocks_T2 + acpc_blocks_T2
 
             pipeline_blocks += anat_blocks_T2
-    
+
     # Anatomical T1 brain extraction
     if not rpool.check_rpool('desc-brain_T1w'):
         anat_brain_blocks = [
@@ -952,9 +956,11 @@ def build_T1w_registration_stack(rpool, cfg, pipeline_blocks=None):
     if not rpool.check_rpool('from-T1w_to-template_mode-image_xfm'):
         reg_blocks = [
             [register_ANTs_anat_to_template, register_FSL_anat_to_template],
-             overwrite_transform_anat_to_template
+            overwrite_transform_anat_to_template,
+
         ]
-        
+
+
     if not rpool.check_rpool('desc-restore-brain_T1w'):
         reg_blocks.append(correct_restore_brain_intensity_abcd)
 
@@ -984,9 +990,14 @@ def build_segmentation_stack(rpool, cfg, pipeline_blocks=None):
         if 'EPI_Template' in cfg.segmentation['tissue_segmentation'][
             'Template_Based']['template_for_segmentation']:
             seg_blocks.append(tissue_seg_EPI_template_based)
-            
+
         pipeline_blocks += seg_blocks
 
+    if cfg.registration_workflows['anatomical_registration']['run'] and 'T1_Template' in cfg.segmentation[
+    'tissue_segmentation']['Template_Based']['template_for_segmentation']:
+        pipeline_blocks.append(warp_Tissuemask_to_T1template)
+
+
     return pipeline_blocks
 
 
@@ -1096,18 +1107,18 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
             func_slice_time,
             func_reorient
         ]
-        
+
         if not rpool.check_rpool('desc-mean_bold'):
             func_preproc_blocks.append(func_mean)
-        
+
         func_mask_blocks = []
         if not rpool.check_rpool('space-bold_desc-brain_mask'):
             func_mask_blocks = [
                 [bold_mask_afni, bold_mask_fsl, bold_mask_fsl_afni,
                  bold_mask_anatomical_refined, bold_mask_anatomical_based,
                  bold_mask_anatomical_resampled, bold_mask_ccs],
                 bold_masking]
-            
+
         func_prep_blocks = [
             calc_motion_stats,
             func_normalize
@@ -1119,7 +1130,7 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
             distcor_blocks.append(distcor_phasediff_fsl_fugue)
 
         if rpool.check_rpool('epi_1'):
-            distcor_blocks.append(distcor_blip_afni_qwarp) 
+            distcor_blocks.append(distcor_blip_afni_qwarp)
             distcor_blocks.append(distcor_blip_fsl_topup)
 
         if distcor_blocks:
@@ -1175,6 +1186,12 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
         ]
         pipeline_blocks += EPI_reg_blocks
 
+    if cfg.registration_workflows['functional_registration']['EPI_registration']['run'
+    ] and 'EPI_Template' in cfg.segmentation['tissue_segmentation']['Template_Based']['template_for_segmentation']:
+        pipeline_blocks.append(warp_Tissuemask_to_EPItemplate)
+
+
+
     # Generate the composite transform for BOLD-to-template for the T1
     # anatomical template (the BOLD-to- EPI template is already created above)
     if cfg.registration_workflows['functional_registration'][
@@ -1255,7 +1272,7 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
     if apply_func_warp:
         pipeline_blocks += [warp_timeseries_to_EPItemplate,
                             warp_bold_mean_to_EPItemplate]
-                            
+
     if not rpool.check_rpool('space-EPItemplate_desc-bold_mask'):
         pipeline_blocks += [warp_bold_mask_to_EPItemplate,
                             warp_deriv_mask_to_EPItemplate]
@@ -1323,7 +1340,21 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
         pipeline_blocks += qc_stack
 
     # Connect the entire pipeline!
-    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
+    try:
+        wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
+    except LookupError as lookup_error:
+        errorstrings = lookup_error.args[0].split('\n')
+        missing_key = errorstrings[
+            errorstrings.index('[!] C-PAC says: The listed resource is not '
+                               'in the resource pool:') + 1]
+        if missing_key.endswith('_bold') and 'func' not in sub_dict:
+            raise FileNotFoundError(
+                'The provided pipeline configuration requires functional '
+                'data but no functional data were found for ' +
+                '/'.join([sub_dict[key] for key in ['site', 'subject_id',
+                         'unique_id'] if key in sub_dict]) + '. Please check '
+                'your data and pipeline configurations.') from lookup_error
+        raise lookup_error
 
     # Write out the data
     # TODO enforce value with schema validation