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cbinyu/apply-gradient-unwarpfield

By cbinyu

•Updated almost 6 years ago

BIDS App to apply a warp field (ie., due to gradient coil non-linearities), to specific image(s)

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cbinyu/apply-gradient-unwarpfield repository overview

⁠apply-gradient-unwarpfield BIDS App

Docker image

This a BIDS App⁠ wrapper that allows you to apply the warp field needed to correct for the gradient non-linearities in MRI images. Like every BIDS App, it consists of a container that includes all of the dependencies and run script that parses a BIDS dataset⁠. BIDS Apps run on Windows, Linux, Mac as well as HCPs/clusters.

⁠Description

apply-gradient-unwarpfield BIDS App will grab all the images for a given subject (or all subjects, if not specified) and apply the unwarping field neccessary to correct for the gradient non-linearity distortions.

It requires that you have the (absolute) full warp field --both in radiological and neurological orientations-- corresponding to your scanner.

This tool will grab the full warp field and convert it to a relative warp field corresponding to each of your images Field of View.

⁠Documentation
⁠Error Reporting

Experiencing problems? Please open an issue⁠ and explain what's happening so we can help.

⁠Usage

This App has the following command line arguments:

usage: run.py [-h]
              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
              --full-warp-folder PATH
              bids_dir output_dir {participant}

Example BIDS App entry point script.

positional arguments:
     bids_dir              The directory with the input dataset formatted
                           according to the BIDS standard.
     output_dir            This argument is here for BIDS-Apps
                           compatibility. All images will be written to the bids_dir
                           overwriting the input.
     {participant}         Level of the analysis that will be performed. Multiple
                           participant level analyses can be run independently
                           (in parallel).

compulsory argument:
     --full-warp-folder PATH
                           Full path to the folder that has both the neurological_
                           and radiological_fullWarp_abs NIfTI images.

optional arguments:
     -h, --help            show this help message and exit
     --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                           The label(s) of the participant(s) that should be
                           analyzed. The label corresponds to
                           sub-<participant_label> from the BIDS spec (so it does
                           not include "sub-"). If this parameter is not provided
                           all subjects will be analyzed. Multiple participants
                           can be specified with a space separated list.
     --skip_bids_validator
                           If set, it will not run the BIDS validator before defacing.

To run it in participant level mode (for one participant) in a Docker container:

docker run -i --rm \
           -v /Users/filo/data/ds005:/bids_dataset \
           cbinyu/apply-gradient-unwarpfield \
               /bids_dataset \
               /bids_dataset/derivatives \
               participant \
               --participant_label 01 \
               --full-warp-folder /path/to/fullWarp/folder

Tag summary

Content type

Image

Digest

Size

169.8 MB

Last updated

almost 6 years ago

docker pull cbinyu/apply-gradient-unwarpfield