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BidsQC

DOI

Using BidsQC

  1. Using either git clone or the download button, copy this repo to the machine you will use for dicom conversion.
  2. Follow the instructions on cbedetti's tutorial to convert the DICOM files to Nifti files. The tutorial is comprehensive and should have all of the information you need. Look at it now.
    1. If you want to (a) convert only a subset of the participant data, or (b) run the conversion on Talapas (the University of Oregon high performance cluster), there are scripts available in the conversion folder of this repo to help you do so. But first, go look at that tutorial.
  3. Check that the results of the conversion and renaming are as expected by using the files in the bidsQC folder of this repo to help you do so.

Overview

The scripts in this repo are a combination of wrappers and quality checking scripts that take neuroimaging files from DICOMS to Niftis named and structured as per BIDS.

Instructions on this page are to run batches of subjects on a high performance cluster running SLURM using a Singularity container of the dcm2Bids package - or - to run the subjects serially on a local machine.

Table of Contents

Dependencies

Repo Contents

Conversion Scripts

These scripts are located in the conversion folder. They allow the user to convert dicoms for only a subset of participants in the dicom directory and to run the conversion on Talapas, the University of Oregon's high performance cluster. The scripts in this repo build off of cbedetti's Dcm2Bids package, which on its own will allow you to convert the DICOM files to Nifti files. See cbedetti's tutorial to learn how to do the basic conversion and for detailed instructions on how to create the configuration file specific to your study's dicoms.

For instructions on how to use the conversion scripts, see the conversion folder README.

bidsQC Scripts

Once Niftis are in BIDS, these scripts can be used to check whether each sequence has the correct number of runs. Files in the target directories are checked against values in the configuration file where the user specifies how many runs of each sequence are expected at each time point. Optional: append the run-## key-value string to file names based on sequence order (option specifed in config file).

For step-by-step instructions and a description of the naming rules, see the bidsQC README.

Final BIDS Steps

Manually Create Metadata Files

As per: http://bids.neuroimaging.io/bids_spec1.0.0-rc2.pdf

Place these files in the top level bids directory.

  • dataset_description.json
  • phasediff.json
  • A JSON for each functional task with TaskName and RepetitionTime
  • README (optional, but strongly recommended)
  • CHANGES (optional, but strongly recommended)

Check the BIDS Conversion

BIDS validator: http://incf.github.io/bids-validator

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Scripts to batch convert dicoms to BIDS in parallel on an HPC environment, followed by a file check

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