adebayobraimah / convert_source Goto Github PK

Perhaps store the relative (or absolute) file paths to for each subject's set of image files mapped to some output filename in a database.

Change MultiBandFactor to MultibandAccelerationFactor in the JSON sidecar.

see this for further details: https://github.com/bids-standard/bids-specification/blob/master/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Change AccelerationFactor to ParallelAcquisitionTechnique in the JSON side car. This element should report a string that yields the name of parallel acquisition type (e.g. GRAPPA or SENSE).

The current (float) value that is reported in the AccelerationFactor field should be renamed to ParallelReductionFactorInPlane.

see reference(s) for details:
https://bids-specification.readthedocs.io/en/latest/04-modality-specific-files/01-magnetic-resonance-imaging-data.html
https://github.com/bids-standard/bids-specification/blob/master/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

As of the current release v0.0.1, no matter the fieldmap case outlined in the BIDS specification docs, the output always corresponds to case 4.

Single band references (sbref) do not appear in output sub-<label>[_ses-<label>]_scans.tsv files.

change acq info to dir, as this is meant to infer direction. In the case of DWIs, use acq-64dirs to denote number of directions.

see this for details: https://github.com/bids-standard/bids-specification/blob/master/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Add TaskName to func json files

Rename _real to _fieldmap in the nifti file renaming functions.

Create wrapper script to recursively walk through directories and create a text file absolute file paths for each subject.

Check if a NIFTI file is already gzipped.

Files with incorrect file extensions cause issues during the BIDS conversion process for NIFTI files.

Add support for re-running the package on converted files identified as unknown.

Will likely need to provide another configuration file to accomplish this. Should likely use either (JSON, easiest - or YAML, most flexible).

Add BIDS renaming utility module/function to rename already converted files.

Create a GUI and a separate set of classes/functions to write configuration files.

Add functionality to rename existing nifti files using the new --nifti option. This should require a separate configuration file with regExs and key words for each modality.

Add options and features for inclusion and exclusion configuration files - such that the config files give regEx strings for each modality.

Replace FSL with Nibabel for several operations used in convertSource.

This is more of a convenience (and will allow this software to be run on windows).

For example a file by DWI_PA.nii.gz is not mapped to sub-00X[_ses-X]_dir-PA_run-0X_dwi.nii.gz provided the mapping [ '_PA' ] to [ 'PA' ].

Add support for function that creates participants.tsv file

Add change log to repo to consistently keep track of changes between versions.

Specify subject and session ID mapping files.

Add support for writing sessions.tsv for each subject for multi-session acquisitions.

tmp_files are mis-labeled during file conversion - thus causing errors.

Convert lowercase custom json sidecar keys to CamelCase.

This is only an issue when using metadata BIDS key words: acq, dir, rec, etc. as these are written to the JSON sidecar.

See bugs outlined and commented here in cs_utils/utils.py.

Add BIDSVersion to JSON sidecar.

The version used here should be BIDS v1.0.2 (I believe).

See this link: https://bids-specification.readthedocs.io/en/latest/03-modality-agnostic-files.html#participants-file