Adding 003 script (running QSIprep recon) to the code directory

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