bids-apps/antscorticalthickness

BIDS App for calculating cortical thickness using ANTs

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.

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-<participant_label> 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

antscorticalthickness's Issues

No valid password to push to docker hub in CI?

https://app.circleci.com/pipelines/github/bids-apps/antsCorticalThickness/14/workflows/edd67b3f-e7ff-4ac7-a336-d054226864fa/jobs/38

Error response from daemon: Get "https://registry-1.docker.io/v2/": unauthorized: incorrect username or password

Exited with code exit status 1

Bids app fails for me!

I'm running the doceker bids app for antscortical thickness on Mac OSX (10.12.6).
Docker version: Version 17.09.0-ce-mac32 (19506)

My command was:

docker run -i --rm -v /Users/davidkennedy/Data/ABCDexample:/bids_dataset:ro -v /Users/davidkennedy/Data/antsoutexample:/outputs bids/antscorticalthickness /bids_dataset /outputs participant --participant_label A107 --n_cpus 3

After some time (~1 hour) , and lots of output to the screen, I get the following error:

ERROR: command exited with nonzero status 1
Command: /usr/lib/ants//antsBrainExtraction.sh -d 3 -a /bids_dataset/sub-A107/anat/sub-A107_T1w.nii.gz -e /opt/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz -f /opt/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumRegistrationMask.nii.gz -m /opt/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz -o /outputs/sub-A107/sub-A107_T1w_ -k 0 -s nii.gz -q 0 -u 1 -z 0

Traceback (most recent call last):
File "/opt/run.py", line 116, in
run(cmd, env={'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS': str(args.n_cpus)})
File "/opt/run.py", line 24, in run
raise Exception("Non zero return code: %d"%process.returncode)
Exception: Non zero return code: 1