From 7bb1b3d7a645452bd23edc4eeb86f64a4ad18e89 Mon Sep 17 00:00:00 2001 From: Allesandra Iadipaolo Date: Thu, 8 Aug 2024 22:13:49 +0000 Subject: [PATCH] Adding 003 script (running QSIprep recon) to the code directory --- code/003_Run_QSI_Recon.sh | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 code/003_Run_QSI_Recon.sh diff --git a/code/003_Run_QSI_Recon.sh b/code/003_Run_QSI_Recon.sh new file mode 100644 index 0000000..86e5f21 --- /dev/null +++ b/code/003_Run_QSI_Recon.sh @@ -0,0 +1,16 @@ +#!/bin/bash +SUBJ=$1 + +#Running QSIPrep reconstruction workflow on two subjects from HBN. + +singularity run \ +~/diffusion_project/my-qsi-prep.sif \ #Path to singularity image path +~/../../tmp/cache/data/ \ #Path to BIDS formatted dataset +~/diffusion_project/results/derivatives/qsirecon \ #Path to output directory +participant \ #Specifying that we want to run on a single subject +--recon_input ~/diffusion_project/results/derivatives/qsiprep \ #Path to results from QSIprep preprocessing +--recon-only \ #Specifying that we only want to run reconstruction +--recon_spec mrtrix_multishell_msmt_pyafq_tractometry \ #Specifying preconfigured reconstruction workflow that we want to use +--participant_label $SUBJ \ #Defining subjectID +--output-resolution 1.8 \ #Specify desired output resolution +--fs-license-file ~/diffusion_project/freesurfer/license.txt #Path to your local copy of Freesurfer license \ No newline at end of file