↔️ Fmriprep Ingress

CHANGELOG.md

@@ -20,6 +20,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Some automatic handling of user-provided BIDSy atlas names.
 - `sig_imports` static method decorator for `Function` nodes, to accommodate type hinting in signatures of `Function` node functions.
+- Ability to ingress an FmriPrep output directory and run derivatives with C-PAC
+- FmripPrep-ingress preconfig that runs derivatives
 - `switch_is_off`, `switch_is_on` and `switch_is_on_off` methods to `Configuration` class
 
 ## Fixed

CPAC/alff/alff.py

@@ -287,8 +287,12 @@ def alff_falff(wf, cfg, strat_pool, pipe_num, opt=None):
             [
                 "space-template_res-derivative_desc-denoisedNofilt_bold",
                 "space-template_res-derivative_desc-preproc_bold",
+                "space-template_desc-preproc_bold"
+            ],
+            [
+                "space-template_res-derivative_desc-bold_mask",
+                "space-template_desc-bold_mask"
             ],
-            "space-template_res-derivative_desc-bold_mask",
         )
     ],
     outputs=["space-template_alff", "space-template_falff"],
@@ -303,14 +307,13 @@ def alff_falff_space_template(wf, cfg, strat_pool, pipe_num, opt=None):
         cfg.amplitude_low_frequency_fluctuation['lowpass_cutoff']
     alff.get_node('hp_input').iterables = ('hp', alff.inputs.hp_input.hp)
     alff.get_node('lp_input').iterables = ('lp', alff.inputs.lp_input.lp)
-
     node, out = strat_pool.get_data(["space-template_res-derivative_desc-denoisedNofilt_bold",
-                                     "space-template_res-derivative_desc-preproc_bold"])
+                                     "space-template_res-derivative_desc-preproc_bold",
+                                     "space-template_desc-preproc_bold"])
     wf.connect(node, out, alff, 'inputspec.rest_res')
-
-    node, out = strat_pool.get_data("space-template_res-derivative_desc-bold_mask")
+    node, out = strat_pool.get_data(["space-template_res-derivative_desc-bold_mask",
+                                     "space-template_desc-bold_mask"])
     wf.connect(node, out, alff, 'inputspec.rest_mask')
-
     outputs = {
         'space-template_alff': (alff, 'outputspec.alff_img'),
         'space-template_falff': (alff, 'outputspec.falff_img')

CPAC/nuisance/bandpass.py

@@ -111,18 +111,28 @@ def bandpass_voxels(realigned_file, regressor_file, bandpass_freqs,
 
         else:
             with open(regressor_file, 'r') as f:
-                header = [f.readline() for x in range(0,3)]
-
-            regressor = np.loadtxt(regressor_file)
+                header = []
+
+                # header wouldn't be longer than 5, right? I don't want to 
+                # loop over the whole file
+                for i in range(5):
+                    line = f.readline()
+                    if line.startswith('#') or isinstance(line[0], str):
+                        header.append(line)
+
+            # usecols=[list]
+            regressor = np.loadtxt(regressor_file, skiprows=len(header))
             Yc = regressor - np.tile(regressor.mean(0), (regressor.shape[0], 1))
             Y_bp = np.zeros_like(Yc)
-            for j in range(regressor.shape[1]):
+
+            # Modify to allow just 1 regressor column
+            shape = regressor.shape[0] if len(regressor.shape) < 1 else regressor.shape[1]
+            for j in range(shape):
                 Y_bp[:, j] = ideal_bandpass(Yc[:, j], sample_period,
                                             bandpass_freqs)
 
             regressor_bandpassed_file = os.path.join(os.getcwd(),
                                     'regressor_bandpassed_demeaned_filtered.1D')
-
             with open(regressor_bandpassed_file, "w") as ofd:
                 # write out the header information
                 for line in header:
@@ -131,7 +141,6 @@ def bandpass_voxels(realigned_file, regressor_file, bandpass_freqs,
                 nuisance_regressors = np.array(Y_bp)
                 np.savetxt(ofd, nuisance_regressors, fmt='%.18f',
                         delimiter='\t')
-
     return bandpassed_file, regressor_bandpassed_file
 
 
@@ -163,4 +172,4 @@ def afni_1dBandpass(in_file, highpass, lowpass, tr=1):
     tr, highpass, lowpass, in_file, out_file)
     os.system(cmd)
 
-    return out_file
+    return out_file

CPAC/pipeline/cpac_pipeline.py

@@ -174,7 +174,8 @@
     erode_mask_boldCSF,
     erode_mask_boldGM,
     erode_mask_boldWM,
-    nuisance_regression_template
+    nuisance_regression_template,
+    ingress_regressors
 )
 
 from CPAC.surface.surf_preproc import surface_postproc
@@ -867,7 +868,8 @@ def build_anat_preproc_stack(rpool, cfg, pipeline_blocks=None):
         pipeline_blocks = []
 
     # T1w Anatomical Preprocessing
-    if not rpool.check_rpool('desc-reorient_T1w'):
+    if not rpool.check_rpool('desc-reorient_T1w') and \
+        not rpool.check_rpool('desc-preproc_T1w'):
         anat_init_blocks = [
             anatomical_init
         ]
@@ -1303,9 +1305,19 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
                           erode_mask_boldCSF,
                           erode_mask_boldGM,
                           erode_mask_boldWM]
-        nuisance += nuisance_masks + choose_nuisance_blocks(cfg, generate_only)
+        nuisance += nuisance_masks + choose_nuisance_blocks(cfg, rpool, \
+                                    generate_only)
 
         pipeline_blocks += nuisance
+
+    pipeline_blocks.append(ingress_regressors)
+
+    # Check for mutually exclusive options
+    if cfg.nuisance_corrections['2-nuisance_regression']['ingress_regressors'] and \
+        cfg.nuisance_corrections['2-nuisance_regression']['create_regressors']:
+        err_msg = "[!] Ingress_regressors and create_regressors can't both run! " \
+                    " Try turning one option off.\n "
+        raise Exception(err_msg)
 
     apply_func_warp = {}
     _r_w_f_r = cfg.registration_workflows['functional_registration']
@@ -1392,8 +1404,9 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
         'nuisance_corrections', '2-nuisance_regression', 'space'
     ] and not generate_only
     if nuisance_template:
-        pipeline_blocks += [(nuisance_regression_template,
-                            ("desc-preproc_bold", "desc-stc_bold"))]
+        pipeline_blocks += [nuisance_regression_template]
+        # pipeline_blocks += [(nuisance_regression_template,
+        #                     ("desc-preproc_bold", "desc-stc_bold"))]
 
     # PostFreeSurfer and fMRISurface
     if not rpool.check_rpool('space-fsLR_den-32k_bold.dtseries'):