hcpbatch's Introduction

hcpbatch

Flexible wrapper for HCP pipeline batch jobs. Adapted from HCP example scripts that are provided with the pipeline. Some of these wrapper scripts rely on features added to my personal fork of the HCP pipelines, and will not work with the official distribution.

Before running, you will need to edit these files for your own installation:

SetUpHCPPipeline.sh : points to local pipeline installation, FSL binaries, etc...
batch_StudySettings.sh : specifies study- or scanner-specific settings (study root directory, final volume and surface resolutions, gradient coefficients, etc...)

General syntax for calling these scripts is: bash <scriptname> <studyname>@<magnetname> <subjectID> ...

If your DICOM session is <dicomfolder>/scan1 <dicomfolder>/scan2 etc., these scripts will import and convert your dicoms into an HCP-friendly file structure:

dicomfolder=/path/to/dicomstorage/mysession
subjectid=101202
study=lifespan@prisma
bash batch_dicom_init.sh $study $dicomfolder $subjectid REST1_AP BOLD=7 SE=8,10
bash batch_anat_dicom_init.sh $study $dicomfolder $subjectid T1=12 T2=14
bash batch_diffusion_dicom_init.sh $study $dicomfolder $subjectid 16 18 20 22

After importing and converting dicoms, you can execute the structural, diffusion, and functional preprocessing pipelines as follows:

bash batch_StructuralPreprocessing.sh $study $subjectid
#Note: You MUST run and complete the structural pipeline before running the diffusion and functional pipelines.
bash batch_DiffusionPreprocessing.sh $study $subjectid
bash batch_FunctionalPreprocessing.sh $study $subjectid

You can also invoke these for multiple subjects to run serially, e.g.,:

bash batch_FunctionalPreprocessing.sh lifespan@prisma "101202 303404 505606"

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