more fixes

aramis-lab · Nov 7, 2024 · 8afcddf · 8afcddf
1 parent b951aad
commit 8afcddf
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/clinica/pipelines/pet_surface/pet_surface_pipeline.py b/clinica/pipelines/pet_surface/pet_surface_pipeline.py
@@ -212,7 +212,7 @@ def _build_input_node_cross_sectional(self):
         if pet_errors:
             all_errors.append(format_clinica_file_reader_errors(pet_errors))
 
-        patterns = [query_pattern_factory(QueryPatternName.T1_FREESURFER_ORIG_NU)]
+        patterns = [query_pattern_factory(QueryPatternName.T1_FREESURFER_ORIG_NU)()]
         patterns.extend(
             [
                 query_pattern_factory(

diff --git a/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py b/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py
@@ -51,7 +51,7 @@ def _build_input_node(self):
         import nipype.pipeline.engine as npe
 
         from clinica.utils.exceptions import ClinicaException
-        from clinica.utils.input_files import t1_volume_dartel_input_tissue
+        from clinica.utils.input_files import QueryPatternName, query_pattern_factory
         from clinica.utils.inputs import clinica_list_of_files_reader
         from clinica.utils.stream import cprint
         from clinica.utils.ux import (
@@ -91,16 +91,18 @@ def _build_input_node(self):
                 fields=self.get_input_fields(), mandatory_inputs=True
             ),
         )
-
+        patterns = [
+            query_pattern_factory(QueryPatternName.T1_VOLUME_DARTEL_INPUT_TISSUE)(
+                tissue_number
+            )
+            for tissue_number in self.parameters["dartel_tissues"]
+        ]
         try:
             d_input = clinica_list_of_files_reader(
                 self.subjects,
                 self.sessions,
                 self.caps_directory,
-                [
-                    t1_volume_dartel_input_tissue(tissue_number)
-                    for tissue_number in self.parameters["dartel_tissues"]
-                ],
+                patterns,
             )
             # d_input is a list of size len(self.parameters['dartel_tissues'])
             #     Each element of this list is a list of size len(self.subjects)

diff --git a/clinica/utils/input_files.py b/clinica/utils/input_files.py
@@ -303,7 +303,7 @@ def get_dwi_preprocessed_brainmask(*args, **kwargs) -> QueryPattern:
 def get_dwi_fmap_phasediff_file(filetype: Union[str, DWIFileType]) -> QueryPattern:
     filetype = DWIFileType(filetype)
     return QueryPattern(
-        f"fmap/sub-*_ses-*_phasediff.{filetype.value}",
+        f"fmap/sub-*_ses-*_phasediff.{filetype.value}*",
         f"phasediff {filetype.value} file",
         "",
     )