Noddi analysis part 3 : Normalization (Warping)

Now that the NODDI maps have been created, we need to normalize them so that they will fit an MNI template in order to do group stats.

Get the Script file

The file warp_NODDI_Singularith.sh is necessary for this step. It works pretty much the same as the files used for preprocessing. - Copy The Warp_template folder in your data folder, along the Preprocessed folder created in step 1 - Copy warp_NODDI_Singularith.sh in your script folder

Use warping Script

You can always start a bash shell in the Singularity container, then use the warping script as described in step 1. Let’s use it directly in Cheaha SLURM:

#!/bin/bash

#SBATCH --partition=short
#SBATCH --cpus-per-task=10
#SBATCH --mem-per-cpu=12000
#SBATCH --time=5:00:00
#SBATCH --array=0-54

cd /data/user/rodolphe/Data/MRST/NODDI/Preprocessed/
readarray -t FILES < <(find . -maxdepth 1 -type d -name 'CBD*' -printf '%P\n')

module load Singularity
cd /data/user/rodolphe/Toolbox/Singularity_images/

srun singularity exec \
--bind /data/user/rodolphe/Data/MRST/NODDI:/data \
--bind /data/user/rodolphe/Scripts/Origin/Szaflarski\ lab/MRST/NODDI/preprocessing:/myscripts \
NODDI_docker.simg bash /myscripts/warp_NODDI_Singularity.sh ${FILES[$SLURM_ARRAY_TASK_ID]}

Warning

Script will create a Noddi_files_warped folder containing the final normalized NODDI FILES