Pull v24.1.2 into main (#821)

* update the VERSION for the next bug fix release (#816)

* [dcm2bids] Remove hardcoded dcm2niix binary to use the value stored in the `converter` Config setting  (#815)

* modifies the dcm2niix command to use the Config converter value instead of hardcoding dcm2niix

* add a check to make sure the converter is a dcm2niix binary

* Pull 24.0.3 in 24.1 release (#820)

* Reload the mri_upload dictionary before checking if a tarchive has been validated (#783)

* reload mri_upload object

* remove debugging exit and print statements

* fix minor bugs when dealing with scans.tsv files (#774)

* fix regex search for excluded series description patterns (#786)

* fix_return_statement_of_create_imaging_upload_dict_from_upload_id_function (#787)

* [dcm2bids] Insert into MRICandidateErrors if there is a Candidate PatientName mismatch (#790)

* insert into MRICandidateErrors when candidate mismatch or pname not matching between DICOMs and NIfTI

* remove exit

* fix table name to MRICandidateErrors instead of MriCandidateErrors as apparently, it makes a difference on MariaDB/Linux VMs while it just worked on local install on Mac... (#793)

* Set DICOM dates to undef if the date does not follow proper DICOM standard (#794)

* set date to undef if it does not follow proper DICOM formats

* fix all dates set to NULL

* Installation and pet fixes (#818)

Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca>

* Update VERSION file for next bug fix release

Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca>
Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca>

Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca>
Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mcgill.ca>

Author: 3 people

VERSION

@@ -1 +1 @@
-24.1.0
+24.1.2

python/lib/dcm2bids_imaging_pipeline_lib/dicom_archive_loader_pipeline.py

@@ -143,8 +143,13 @@ def _run_dcm2niix_conversion(self):
         nifti_tmp_dir = os.path.join(self.tmp_dir, "nifti_files")
         os.makedirs(nifti_tmp_dir)
 
+        converter = self.config_db_obj.get_config("converter")
+        if not re.search('.*dcm2niix.*', converter, re.IGNORECASE):
+            message = f"{converter} does not appear to be a dcm2niix binary."
+            self.log_error_and_exit(message, lib.exitcode.PROJECT_CUSTOMIZATION_FAILURE, is_error="Y", is_verbose="N")
+
         dcm2niix_process = subprocess.Popen(
-            ["dcm2niix", "-ba", "n", "-z", "y", "-o", nifti_tmp_dir, self.extracted_dicom_dir],
+            [converter, "-ba", "n", "-z", "y", "-o", nifti_tmp_dir, self.extracted_dicom_dir],
             stdout=subprocess.PIPE,
             stderr=subprocess.STDOUT
         )

uploadNeuroDB/NeuroDB/ImagingUpload.pm

@@ -643,11 +643,12 @@ sub HrrtPatientNameMatch {
     # if the filename name matches one of the following, return 1 as the patient
     # name will not be in the filename anyway
     my $exclude_regex = "blank|phantom|temp|test|tar|noisytx|"
-                        . "script|ini|directnorm|up_mask";
+                        . "script|ini|directnorm|up_mask|To_Archive|mask_input";
     return 1 if ( $filename =~ /$exclude_regex/i );
 
     # if the patient name matches with the filename return 1, otherwise return 0
-    ( $filename =~ /$this->{'pname'}/i ) ? return 1 : return 0;
+    my $parsed_filename = $filename =~ s/-/_/r;
+    ( $parsed_filename =~ /$this->{'pname'}/i ) ? return 1 : return 0;
 }