AFNI 3dDespike in template space (#1813)

Author: shnizzedy

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 - Added the ability to downsample to 10K or 2K resolution for freesurfer runs
+- Added the ability to run AFNI 3dDespike on template-space BOLD data.
 - Added the ability to ingress TotalReadoutTime from epi field map meta-data from the JSON sidecars.
 - Added the ability to use TotalReadoutTime of epi field maps in the calculation of FSL topup distortion correction.
 - Difference method (``-``) for ``CPAC.utils.configuration.Configuration`` instances

CPAC/func_preproc/func_preproc.py

@@ -1003,8 +1003,8 @@ def func_despike(wf, cfg, strat_pool, pipe_num, opt=None):
     {"name": "func_despike",
      "config": ["functional_preproc", "despiking"],
      "switch": ["run"],
-     "option_key": "None",
-     "option_val": "None",
+     "option_key": ["space"],
+     "option_val": ["native"],
      "inputs": ["desc-preproc_bold"],
      "outputs": {
          "desc-preproc_bold": {
@@ -1030,6 +1030,37 @@ def func_despike(wf, cfg, strat_pool, pipe_num, opt=None):
     return (wf, outputs)
 
 
+def func_despike_template(wf, cfg, strat_pool, pipe_num, opt=None):
+    '''
+    {"name": "func_despike_template",
+     "config": ["functional_preproc", "despiking"],
+     "switch": ["run"],
+     "option_key": ["space"],
+     "option_val": ["template"],
+     "inputs": ["space-template_desc-preproc_bold"],
+     "outputs": {
+         "space-template_desc-preproc_bold": {
+             "Description": "De-spiked BOLD time-series via AFNI 3dDespike."
+    }}}
+    '''
+
+    despike = pe.Node(interface=preprocess.Despike(),
+                      name=f'func_despiked_template_{pipe_num}',
+                      mem_gb=0.66,
+                      mem_x=(8251808479088459 / 1208925819614629174706176,
+                             'in_file'))
+    despike.inputs.outputtype = 'NIFTI_GZ'
+
+    node, out = strat_pool.get_data("space-template_desc-preproc_bold")
+    wf.connect(node, out, despike, 'in_file')
+
+    outputs = {
+        'space-template_desc-preproc_bold': (despike, 'out_file')
+    }
+
+    return (wf, outputs)
+
+
 def func_slice_time(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     {"name": "func_slice_time",

CPAC/pipeline/cpac_pipeline.py

@@ -127,6 +127,7 @@
     func_scaling,
     func_truncate,
     func_despike,
+    func_despike_template,
     func_slice_time,
     func_reorient,
     bold_mask_afni,
@@ -1284,7 +1285,9 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
     if not rpool.check_rpool('space-template_desc-bold_mask'):
         pipeline_blocks += [warp_bold_mask_to_T1template,
                             warp_deriv_mask_to_T1template]
-        
+
+    pipeline_blocks += [func_despike_template]
+
     target_space_alff = cfg.amplitude_low_frequency_fluctuation['target_space']
     if 'Template' in target_space_alff and not rpool.check_rpool('space-template_desc-denoisedNofilt_bold'):
         pipeline_blocks += [warp_denoiseNofilt_to_T1template]

CPAC/pipeline/schema.py

@@ -630,7 +630,8 @@ def sanitize(filename):
             'scaling_factor': Number
         },
         'despiking': {
-            'run': forkable
+            'run': forkable,
+            'space': In({'native', 'template'})
         },
         'slice_timing_correction': {
             'run': forkable,

CPAC/resources/configs/pipeline_config_blank.yml

@@ -1192,6 +1192,8 @@ functional_preproc:
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [Off]
 
+    space: 'native'
+
 nuisance_corrections:
   2-nuisance_regression:
 

CPAC/resources/configs/pipeline_config_rbc-options.yml

@@ -110,6 +110,7 @@ functional_preproc:
     # this is a fork point
     #   run: [On, Off] - this will run both and fork the pipeline
     run: [On]
+    space: 'template'
 
 nuisance_corrections:
   2-nuisance_regression: