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### How to run this walkthrough | ||
# XCP-D Walkthrough | ||
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1. Open terminal | ||
2. Navigate to where you want your XCP-D runs, and create a folder called `XCPD_test` | ||
3. Navigate into this folder: `cd XCPD_test` | ||
4. Download the singularity image: `singularity build xcp_walkthrough.sif docker://pennlinc/xcp_walkthrough:main` | ||
5. Run the walkthrough! | ||
``` | ||
This repository defines a Docker image containing XCP-D and example data. | ||
When you run the Docker image, it will apply XCP-D to the example data and write out XCP-D derivatives. | ||
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The example data are located in `/data/EF/derivatives/fmriprep` within the Docker image. | ||
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**NOTE**: You will need to provide your own FreeSurfer license (labeled `<path_to_Freesurfer_license_file>` below). | ||
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## How to run this walkthrough | ||
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1. Open terminal | ||
2. Navigate to where you want your XCP-D outputs to be generated (labeled `<path_to_test_folder>` below). | ||
3. Download the container: | ||
- For Singularity: `singularity build xcp_walkthrough.sif docker://pennlinc/xcp_walkthrough:main` | ||
- For Docker: `docker pull pennlinc/xcp_walkthrough:main` | ||
4. Run the walkthrough! | ||
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### Singularity command | ||
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```bash | ||
#$ -l h_vmem=40G # Allot at least 40G; this is the format for submitting via an SGE cluster | ||
singularity run --cleanenv -B ~/XCPD_test ~/XCPD_test/xcp_walkthrough.sif /data/EF/derivatives/fmriprep ~/XCPD_test/output --fs-license-file <path_to_Freesurfer_license_file> participant -vv | ||
singularity run --cleanenv \ | ||
-B <path_to_test_folder> \ | ||
<path_to_test_folder>/xcp_walkthrough.sif \ | ||
/data/EF/derivatives/fmriprep \ | ||
<path_to_test_folder>/output \ | ||
--fs-license-file <path_to_Freesurfer_license_file> \ | ||
participant \ | ||
-vv | ||
``` | ||
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### Docker command | ||
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```bash | ||
docker run --rm -ti \ | ||
-v <path_to_test_folder>:/out \ | ||
-v <path_to_Freesurfer_license_file>:/license.txt \ | ||
pennlinc/xcp_walkthrough:main \ | ||
/data/EF/derivatives/fmriprep \ | ||
/out \ | ||
--fs-license-file /license.txt \ | ||
participant \ | ||
-vv | ||
``` |