https://github.com/bids-apps/antsCorticalThickness

BIDS App for calculating cortical thickness using ANTs
https://github.com/bids-apps/antsCorticalThickness

bids bidsapp

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BIDS App for calculating cortical thickness using ANTs

• Host: GitHub
• URL: https://github.com/bids-apps/antsCorticalThickness
• Owner: bids-apps
• License: apache-2.0
• Created: 2017-10-13T19:36:36.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2024-04-30T09:47:35.000Z (5 months ago)
• Last Synced: 2024-06-21T03:10:08.054Z (3 months ago)
• Topics: bids, bidsapp
• Language: Python
• Homepage:
• Size: 39.1 KB
• Stars: 0
• Watchers: 5
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bids - antsCorticalThickness

README

        
## BIDS App for calculating cortical thickness using ANTs

This BIDS App runs ANTs cortical thickness estimation pipeline.

For more information about the specification of BIDS Apps see [here](https://docs.google.com/document/d/1E1Wi5ONvOVVnGhj21S1bmJJ4kyHFT7tkxnV3C23sjIE/edit#).

### Description

The app finds all T1w files for each subject and runs antsCorticalThickness.sh (if there is only one T1w file per subject) or

antsLongitudinalCorticalThickness.sh (if there are more than one T1w files).

### Documentation

https://github.com/ANTsX/ANTs

### How to report errors

https://github.com/BIDS-Apps/antsCorticalThickness/issues

### Acknowledgements

https://github.com/ANTsX/ANTs#boilerplate-ants

### Usage

This App has the following command line arguments:

		usage: run.py [-h]

                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]

                  [--n_cpus N_CPUS]

                  [--stage {brain_extraction,template_registration,tissue_segmentation,qc,cortical_thickness}]

                  [-v]

                  bids_dir output_dir {participant}

    Cortical thickness estimation using ANTs.

    positional arguments:

      bids_dir              The directory with the input dataset formatted

                            according to the BIDS standard.

      output_dir            The directory where the output files should be stored.

                            If you are running group level analysis this folder

                            should be prepopulated with the results of

                            theparticipant level analysis.

      {participant}         Level of the analysis that will be performed. Multiple

                            participant level analyses can be run independently

                            (in parallel) using the same output_dir.

    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- from the BIDS spec (so it does

                            not include "sub-"). If this parameter is not provided

                            all subjects should be analyzed. Multiple participants

                            can be specified with a space separated list.

      --n_cpus N_CPUS       Number of CPUs/cores available to use.

      --stage {brain_extraction,template_registration,tissue_segmentation,qc,cortical_thickness}

                            Which stage of ACT to run

      -v, --version         show program's version number and exit

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

    docker run -i --rm \

		-v /Users/filo/data/ds005:/bids_dataset:ro \

		-v /Users/filo/outputs:/outputs \

		bids/antscorticalthickness \

		/bids_dataset /outputs participant --participant_label 01