MIRIAD converter to BIDS #1290
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MIRIAD converter to BIDS #1290
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Status right now:
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AliceJoubert
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Sep 9, 2024
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Thanks for the work @MatthieuJoulot ! I made a few... lots of comments actually ^^'. Tell me if you need clarification.
| return value | ||
| raise ValueError( | ||
| f"BIDS MIRIAD subject ID {value} is not properly formatted. " | ||
| "Expecting a 'sub-MIRIAD' format." |
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Suggested change
| "Expecting a 'sub-MIRIAD' format." | |
| "Expecting a 'sub-MIRIADXXX' format." |
| @@ -319,6 +321,29 @@ def from_original_study_id(cls, study_id: str) -> str: | |||
| def to_original_study_id(self) -> str: | |||
| return str(self.replace("sub-", "")) | |||
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| class MIRIADBIDSSubjectID(BIDSSubjectID): | |||
| """Implementation for MIRIAD of the BIDSSubjectIDClass, allowing to go from the source id MIRIAD### | |||
| to a bids id sub-MIRAD### and reciprocally.""" | |||
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Suggested change
| to a bids id sub-MIRAD### and reciprocally.""" | |
| to a bids id sub-MIRIAD### and reciprocally.""" |
| return f"sub-{study_id}" | ||
| raise ValueError( | ||
| f"Raw MIRIAD subject ID {study_id} is not properly formatted. " | ||
| "Expecting a 'Y' format." |
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| "Expecting a 'Y' format." | |
| "Expecting a 'MIRIADXXX' format." |
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| input_dir = 'your_input_directory' # Where the original data is located | ||
| output_dir = 'your_output_directory' # Where the BIDS data will be written | ||
| csv_file = 'metadata.csv' # Metadata CSV file to store extracted information |
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| input_dir = 'your_input_directory' # Where the original data is located | |
| output_dir = 'your_output_directory' # Where the BIDS data will be written | |
| csv_file = 'metadata.csv' # Metadata CSV file to store extracted information |
You can directly use the paths given to the convert function :
- input_dir < > path_to_dataset
- output_dir < > bids_dir
And if you use 'metadata.csv' only once I would not define a variable specifically for this, you can use it as is inside convert
| subjects (Optional[UserProvidedPath], optional): _description_. Defaults to None. | ||
| n_procs (Optional[int], optional): _description_. Defaults to 1. | ||
| """ | ||
| from clinica.iotools.converters.miriad_to_bids.miriad_to_bids_utils import create_bids_structure |
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| from clinica.iotools.converters.miriad_to_bids.miriad_to_bids_utils import create_bids_structure | |
| from clinica.iotools.converters.miriad_to_bids.miriad_to_bids_utils import create_bids_structure | |
| from ..utils import validate_input_path | |
| path_to_dataset = validate_input_path(path_to_dataset) | |
| bids_dir = validate_input_path(bids_dir, check_exist=False) | |
| if n_procs != 1: | |
| cprint( | |
| f"{get_converter_name(StudyName.MIRIAD)} converter does not support multiprocessing yet. n_procs set to 1.", | |
| lvl="warning", | |
| ) | |
| if not subjects: | |
| #todo |
First step there would be to check the inputs of the convert function :
- your paths : the function given here verify existence go the path if needed and return a Path object, so we are sure we get always the same type of objects when it comes to user-given paths.
- optional parameters : n_procs is not implemented (and I doubt you want to) so we just warn the user if she/he tries to use it. Should be the same for subjects 😁
Makes me wonder though, you do not plan on using any clinical data as an input ?
| input_file = os.path.join(root, file) | ||
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| # Create BIDS structure and move the file | ||
| create_bids_structure(subject_id, session, cohort, diagnosis, gender, input_file, path_to_dataset, bids_dir, path_to_clinical) |
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| create_bids_structure(subject_id, session, cohort, diagnosis, gender, input_file, path_to_dataset, bids_dir, path_to_clinical) | |
| create_bids_structure(subject_id, session, file_path, bids_dir) |
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| bids_filename = f"sub-{subject_id}_ses-{session}_T1w.nii.gz" | ||
| output_file = os.path.join(f"sub-{subject_id}", f"ses-{session}", 'anat', bids_filename) |
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| bids_filename = f"sub-{subject_id}_ses-{session}_T1w.nii.gz" | |
| output_file = os.path.join(f"sub-{subject_id}", f"ses-{session}", 'anat', bids_filename) | |
| output_file = f"sub-MIRIAD{subject_id}/ses-{session}/anat/sub-MIRIAD{subject_id}_ses-{session}_T1w.nii.gz" |
| parts = file.split('_') | ||
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| # Extract information from filename | ||
| cohort = parts[0] # miriad |
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| cohort = parts[0] # miriad |
If it is always the same as I assumed above in my regex you do not need to retrieve the info anymore
| # Write the extracted information to CSV | ||
| bids_filename = f"sub-{subject_id}_ses-{session}_T1w.nii.gz" | ||
| output_file = os.path.join(f"sub-{subject_id}", f"ses-{session}", 'anat', bids_filename) | ||
| csvwriter.writerow([cohort, subject_id, diagnosis, gender, session, input_file, output_file]) |
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Do you want the "subject_id" to be MIRIADXXX or XXX ?
| ) | ||
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| @classmethod | ||
| def from_original_study_id(cls, study_id: str) -> str: |
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As written you should have ids of 3 digits always (so there would need to be a padding if it can be 1 or 2). Though I don't think you are using that class for now
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Alright clinical data have been added |
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Implementation of a BIDS converter for the MIRIAD cohort.