WIP fix: skip hmc on 3D PET

Author: Murat Bilgel

petprep/utils/misc.py

@@ -78,7 +78,14 @@ def estimate_pet_mem_usage(pet_fname: str) -> tuple[int, dict]:
     nvox = int(np.prod(img.shape, dtype='u8'))
     # Assume tools will coerce to 8-byte floats to be safe
     pet_size_gb = 8 * nvox / (1024**3)
-    pet_tlen = img.shape[-1]
+
+    if img.ndim == 4:
+        pet_tlen = img.shape[3]
+    elif img.ndim == 3:
+        pet_tlen = 1
+    else:
+        raise ValueError('PET image must be 3D or 4D')
+
     mem_gb = {
         'filesize': pet_size_gb,
         'resampled': pet_size_gb * 4,

petprep/workflows/pet/base.py

@@ -166,11 +166,6 @@ def init_pet_wf(
     all_metadata = [config.execution.layout.get_metadata(file) for file in pet_series]
 
     nvols, mem_gb = estimate_pet_mem_usage(pet_file)
-    if nvols <= 1 - config.execution.sloppy:
-        config.loggers.workflow.warning(
-            f'Too short PET series (<= 5 timepoints). Skipping processing of <{pet_file}>.'
-        )
-        return
 
     config.loggers.workflow.debug(
         'Creating pet processing workflow for <%s> (%.2f GB / %d frames). '

petprep/workflows/pet/fit.py

@@ -20,6 +20,7 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
+import os
 from pathlib import Path
 
 import nibabel as nb
@@ -198,12 +199,17 @@ def init_pet_fit_wf(
     )
     hmc_buffer = pe.Node(niu.IdentityInterface(fields=['hmc_xforms']), name='hmc_buffer')
 
+    if pet_tlen <= 1:
+        # 3D PET
+        petref = pet_file
+        hmc_xforms = Path(os.getenv('FSLDIR')) / 'etc' / 'flirtsch' / 'ident.mat'
+        config.loggers.workflow.debug('3D PET file - motion correction not needed')
     if petref:
         petref_buffer.inputs.petref = petref
-        config.loggers.workflow.debug('Reusing motion correction reference: %s', petref)
+        config.loggers.workflow.debug('(Re)using motion correction reference: %s', petref)
     if hmc_xforms:
         hmc_buffer.inputs.hmc_xforms = hmc_xforms
-        config.loggers.workflow.debug('Reusing motion correction transforms: %s', hmc_xforms)
+        config.loggers.workflow.debug('(Re)using motion correction transforms: %s', hmc_xforms)
 
     timing_parameters = prepare_timing_parameters(metadata)
     frame_durations = timing_parameters.get('FrameDuration')