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
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