PyPI 官网下载 | bidsphysio-4.0rc1.tar.gz

# bidsphysio Converts physio data (CMRR, AcqKnowledge, Siemens PMU) to BIDS physiological recording [](https://hub.docker.com/r/cbinyu/bidsphysio/tags/) [](https://travis-ci.com/cbinyu/bidsphysio) [](https://codecov.io/gh/cbinyu/bidsphysio) [](https://zenodo.org/badge/latestdoi/239006399) ## Usage ``` physio2bidsphysio --infile <physiofiles> --bidsprefix <Prefix> [--verbose] ``` Example: ``` physio2bidsphysio --infile 07+epi_MB4_2mm_Physio+00001.dcm \ --bidsprefix BIDSfolder/sub-01/func/sub-01_task-REST_run-1 ``` ## Arguments * `<physiofiles>` space-separated files with the physiological recordings (formats: * `<.dcm>`: DICOM file with physiological recording from a CMRR Multi-Band sequence (only a single one for this file type). * `<.acq>`: AcqKnowledge file (BioPac). * `<.puls>` or `<.resp>`: Siemens PMU file (VB15A, VBX, VE11C). * `<Prefix>` is the prefix that will be used for the BIDS physiology files. If all physiological recordings have the same sampling rate and starting time, the script will save the files: `<Prefix>_physio.json` and `<Prefix>_physio.tsv.gz`. If the physiological signals have different sampling rates and/or starting times, the script will save the files: `<Prefix>_recording-<label>_physio.json` and `<Prefix>_recording-<label>_physio.tsv.gz`, with the corresponding labels (e.g., `cardiac`, `respiratory`, etc.). * `--verbose` will print out some warning messages. Note: If desired, you can use the corresponding `_bold.nii.gz` BIDS file as `--bidsprefix`. The script will strip the `_bold.nii.gz` part from the filename and use what is left as `<Prefix>`. This way, you can assure that the output physiology files match the `_bold.nii.gz` file for which they are intended. ## Installation You can install the tool by downloading the package and installing it with `pip`: ``` mkdir /tmp/bidsphysio && \ curl -sSL https://github.com/cbinyu/bidsphysio/archive/master.tar.gz \ | tar -vxz -C /tmp/bidsphysio --strip-components=1 && \ cd /tmp/bidsphysio && \ pip install . && \ cd / && \ rm -rf /tmp/bidsphysio ``` ## Docker usage ``` docker run [docker options] cbinyu/bidsphysio \ --infile <physiofiles> \ --bidsprefix <Prefix> ``` Note that the `<physiofiles>` and the `<Prefix>` should use the corresponding paths inside the Docker container. Example: ``` docker run --rm \ --user $(id -u):$(id -g) \ --name test_bidsphysio \ --volume /tmp:/tmp \ cbinyu/bidsphysio \ --infile /tmp/07+epi_MB4_2mm_Physio+00001.dcm \ --bidsprefix /tmp/test ``` ## Alternative use: The tool will also install the binaries: `dcm2bidsphysio`, `acq2bidsphysio` and `pmu2bidsphysio`, to extract a specific file type. ``` dcm2bidsphysio --infile <DCMfile> --bidsprefix <Prefix> acq2bidsphysio --infile <acqfiles> --bidsprefix <Prefix> pmu2bidsphysio --infile <pmufiles> --bidsprefix <Prefix> ``` ## How to use in your own Python program After installing the module using `pip` (see [above](https://github.com/cbinyu/bidsphysio#installation "Installation") ), you can use it in your own Python program this way: ``` from bidsphysio import dcm2bidsphysio dcm2bidsphysio.dcm2bids( dicom_file, prefix ) ``` or: ``` from bidsphysio import acq2bidsphysio acq2bidsphysio.acq2bids( [acq_files], prefix ) ``` or: ``` from bidsphysio import pmu2bidsphysio pmu2bidsphysio.pmu2bids( [pmu_files], prefix ) ```