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Convert source DICOM, PAR REC or NIFTI image data to BIDS directory layout

License: GNU General Public License v3.0

Python 96.86% TeX 0.09% Shell 3.05%

mri dicom parrec nifti bids imaging data-sharing data-standards brain-imaging par rec conversion pet

convert_source's Introduction

convert_source

Convert source DICOM, PAR REC or NIFTI image data to BIDS directory layout.

The YAML configuration file used as input dictates the search terms used to find and rename files. Please see config/config.default.yml or config/config.example.yml for examples.

Requires dcm2niix and pydicom.

usage: study_proc [-h] [-s STUDY_DIR] [-o OUT_DIR] [-c CONFIG.yml] [--no-gzip]
                  [--compress INT] [--zero-pad INT] [--append-dwi-info]
                  [--verbose] [--version] [--path-env PATH_VAR]

Convert source data of a study's imaging data to BIDS NIFTI data.

optional arguments:
  -h, --help            show this help message and exit

Required Argument(s):
  -s STUDY_DIR, -study STUDY_DIR, --study-dir STUDY_DIR
                        Parent study image directory for all subjects.
  -o OUT_DIR, -out OUT_DIR, --out-dir OUT_DIR
                        Output directory.

Optional Argument(s):
  -c CONFIG.yml, -config CONFIG.yml, --config-file CONFIG.yml
                        Input YAML configuration file. If no configuration
                        file is provided, then the default configuration file
                        is used.
  --no-gzip             DO NOT gzip the resulting BIDS NIFTI files [default:
                        False].
  --compress INT        Compression level [1 - 9] - 1 is fastest, 9 is
                        smallest [default: 6].
  --zero-pad INT        The amount of zeropadding to pad the run numbers of
                        the BIDS NIFTI files (e.g. '--zero-pad=2' corresponds
                        to '01') [default: 2].
  --append-dwi-info     RECOMMENDED: Appends DWI acquisition information
                        (unique non-zero b-values, and TE, in msec.) to BIDS
                        acquisition filename of diffusion weighted image files
                        [default: False].
  --verbose             Enables verbose output to the command line.
  --version             Prints the version of 'convert_source', then exits.

Expert Option(s):
  --path-env PATH_VAR   Environmental path variable or variables for
                        dependencies (e.g. the path to 'dcm2niix'). NOTE: This
                        option is repeatable, and can thus be specified
                        multiple times.

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convert_source's Issues

Check if a file is already gzipped

Check if a NIFTI file is already gzipped.

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

Prevent the package from converting data that has already been processed.

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.

Add `BIDSVersion` to JSON sidecar

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

Specify subject and session ID mapping files

Specify subject and session ID mapping files.

tmp_files are mis-labeled during file conversion

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

Wrapper to obtain full file paths

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

BIDS file renaming utility

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

Convert lower case custom json sidecar keys to camel case

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.

Single band references do not appear in output scans TSV files

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

Add support for re-running with files identified as 'unknown'

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).

Fieldmaps are not processed correctly

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.

Add support for participants TSV

Add support for function that creates participants.tsv file

Add options for inclusion and exclusion

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

Change 'MultiBandFactor' to 'MultibandAccelerationFactor'

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

Add 'Nifti' file rename option

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.

BIDS related file searches are not mapped to BIDS descriptive terms

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' ].

Rename '_real' to '_fieldmap'

Rename _real to _fieldmap in the nifti file renaming functions.

Address BUGs outlined in cs_utils

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

Add 'TaskName' to func json files

Add TaskName to func json files

Add support for sessions TSV

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

Replace FSL dependencies with Nibabel in source code

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).

Add `CHANGELOG` to Repo

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

Change 'AccelerationFactor' to 'ParallelAcquisitionTechnique'

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

change acq info to dir

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

GUI to write configuration file

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