some more fixes

aramis-lab · Nov 7, 2024 · b951aad · b951aad
1 parent eb5dba8
commit b951aad
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Showing 3 changed files with 22 additions and 21 deletions.
diff --git a/clinica/pipelines/dwi/preprocessing/fmap/pipeline.py b/clinica/pipelines/dwi/preprocessing/fmap/pipeline.py
@@ -139,9 +139,7 @@ def _build_input_node(self):
         if len(self.subjects):
             print_images_to_process(self.subjects, self.sessions)
             cprint(
-                f"List available in {self.base_dir / self.name / 'participants.tsv'}"
-            )
-            cprint(
+                f"List available in {self.base_dir / self.name / 'participants.tsv'}\n"
                 "Computational time will depend of the number of volumes in your DWI dataset and the use of CUDA."
             )
 

diff --git a/clinica/pipelines/statistics_surface/pipeline.py b/clinica/pipelines/statistics_surface/pipeline.py
@@ -114,6 +114,7 @@ def get_output_fields(self) -> List[str]:
     def _build_input_node(self):
         """Build and connect an input node to the pipeline."""
         from clinica.utils.exceptions import ClinicaException
+        from clinica.utils.input_files import QueryPattern
         from clinica.utils.inputs import clinica_list_of_files_reader
 
         # Check if already present in CAPS
@@ -133,26 +134,28 @@ def _build_input_node(self):
             )
 
         # Check input files
-        surface_query = []
+        patterns: list[QueryPattern] = []
         # clinica_files_reader expects regexp to start at subjects/ so sub-*/ses-*/ is removed here
         fwhm = str(self.parameters["full_width_at_half_maximum"])
         for direction, hemi in zip(["left", "right"], ["lh", "rh"]):
             cut_pattern = "sub-*/ses-*/"
             query = {"subject": "sub-*", "session": "ses-*", "hemi": hemi, "fwhm": fwhm}
             pattern_hemisphere = self.parameters["custom_file"] % query
-            surface_based_info = {
-                "pattern": pattern_hemisphere[
-                    pattern_hemisphere.find(cut_pattern) + len(cut_pattern) :
-                ],
-                "description": f"surface-based features on {direction} hemisphere at FWHM = {fwhm}",
-            }
-            surface_query.append(surface_based_info)
+            patterns.append(
+                QueryPattern(
+                    pattern_hemisphere[
+                        pattern_hemisphere.find(cut_pattern) + len(cut_pattern) :
+                    ],
+                    f"surface-based features on {direction} hemisphere at FWHM = {fwhm}",
+                    "",
+                )
+            )
         try:
             clinica_list_of_files_reader(
                 self.subjects,
                 self.sessions,
                 self.caps_directory,
-                surface_query,
+                patterns,
             )
         except ClinicaException as e:
             raise RuntimeError(e)

diff --git a/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_pipeline.py b/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_pipeline.py
@@ -49,9 +49,9 @@ def _build_input_node(self):
         import nipype.interfaces.utility as nutil
         import nipype.pipeline.engine as npe
 
-        from clinica.utils.exceptions import ClinicaCAPSError, ClinicaException
-        from clinica.utils.input_files import t1_volume_template_tpm_in_mni
-        from clinica.utils.inputs import clinica_file_filter, clinica_file_reader
+        from clinica.utils.exceptions import ClinicaException
+        from clinica.utils.input_files import QueryPatternName, query_pattern_factory
+        from clinica.utils.inputs import clinica_file_filter
         from clinica.utils.stream import cprint
         from clinica.utils.ux import (
             print_groups_in_caps_directory,
@@ -66,16 +66,16 @@ def _build_input_node(self):
                 f"Group {self.parameters['group_label']} does not exist. "
                 "Did you run t1-volume or t1-volume-create-dartel pipeline?"
             )
-
+        pattern = query_pattern_factory(QueryPatternName.T1_VOLUME_TEMPLATE_TPM_IN_MNI)(
+            group_label=self.parameters["group_label"],
+            tissue_number=1,
+            modulation=self.parameters["modulate"],
+        )
         gm_mni, self.subjects, self.sessions = clinica_file_filter(
             self.subjects,
             self.sessions,
             self.caps_directory,
-            t1_volume_template_tpm_in_mni(
-                group_label=self.parameters["group_label"],
-                tissue_number=1,
-                modulation=self.parameters["modulate"],
-            ),
+            pattern,
         )
 
         read_parameters_node = npe.Node(