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README.md

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+## 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-<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