Add README and example scripts

ce355fce · Matthew K Defenderfer · e8f5e10e · ce355fce · ce355fce · ce355fce
Commit ce355fce authored Jun 18, 2021 by Matthew K Defenderfer
5 changed files
--- a/README.txt
+++ b/README.txt
+This project stores preprocessing and processing code for performing NODDI analysis (Zhang et al. 2011) at the PRL, URL, and LPZ in macular degeneration participants. Included are scripts setting up preprocessing using a basic FSL pipeline including topup and eddy. b0 images come from the diffusion scans themselves as opposed to SpinEcho fieldmaps. The NODDI toolbox used is version 1.01 that has been modified to remove status bar graphics and allow the pipeline to be run completely from the command line without needing the MATLAB GUI.
+
+Scripts of interest are diff_preprocess.m that does basic file management and sets up the bash script to perform topup and eddy as well as noddi_MASTER that sets up the bash script to run NODDI. 
+
+Example preprocessing, NODDI processing, and registration scripts can be found in example-bash-scripts for one subject.
--- a/diff_preprocess.m
+++ b/diff_preprocess.m
@@ -11,7 +11,7 @@ A bash script will be written and will perform both topup and eddy on each
 pair of scans.
 %}

-% make the given directories
+% make the raw and FSL directories for the given subject. On
 if ~exist(fullfile(subdir,subj,'raw','dir98'),'dir')
    mkdir(fullfile(subdir,subj,'raw','dir98'))
 end

--- a/example-bash-scripts/sub-MDP001-dwi-FSL-preproc.sh
+++ b/example-bash-scripts/sub-MDP001-dwi-FSL-preproc.sh
+#!/bin/bash
+#SBATCH --partition=medium
+#SBATCH --time=24:00:00
+#SBATCH --ntasks=5
+#SBATCH --mem-per-cpu=8G
+#SBATCH --output=/data/user/mdefende/datasets/MDP-diff/jobs/sub-MDP001-dwi-FSL-preproc.txt
+
+module load FSL/6.0.3
+
+# Extract b0 images from AP and PA scans for both dir98 and dir99. Save in FSL directory
+fslroi /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-AP_run-01_dwi.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_b0 0 1
+
+fslroi /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-PA_run-01_dwi.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/PA_b0 0 1
+
+fslmerge -t /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/both_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/PA_b0
+
+
+fslroi /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-AP_run-01_dwi.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/AP_b0 0 1
+
+fslroi /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-PA_run-01_dwi.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/PA_b0 0 1
+
+fslmerge -t /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/both_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/AP_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/PA_b0
+
+# Create the acqparams.txt files 
+printf "0 -1 0 0.112 \n0 1 0 0.112" > /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/acqparams.txt
+printf "0 -1 0 0.112 \n0 1 0 0.112" > /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/acqparams.txt
+
+# run topup for both dir98 and dir99
+topup --imain=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/both_b0 --datain=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/acqparams.txt --config=b02b0.cnf  --out=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/topup_AP_PA_b0 --iout=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0  --fout=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/fout
+
+topup --imain=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/both_b0 --datain=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/acqparams.txt --config=b02b0.cnf  --out=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/topup_AP_PA_b0 --iout=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0  --fout=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/fout
+
+# Perform brain extraction for both dir98 and dir99
+fslmaths /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0 -Tmean /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0
+bet /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0_brain -m
+
+fslmaths /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0 -Tmean /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0
+bet /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0_brain -m
+
+# Merge raw PA to raw AP
+fslmerge -t /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_raw /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-AP_run-01_dwi.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-PA_run-01_dwi.nii.gz
+fslmerge -t /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/sub-MDP001-AP_PA_dir99_raw /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-AP_run-01_dwi.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-PA_run-01_dwi.nii.gz
+
+# Merge AP and PA bvals files
+paste -d ' ' /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-AP_run-01_dwi.bval /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-PA_run-01_dwi.bval > /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_PA_dir98.bval
+
+paste -d ' ' /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-AP_run-01_dwi.bval /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-PA_run-01_dwi.bval > /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/AP_PA_dir99.bval
+
+# Merge AP and PA bvecs files
+paste -d ' ' /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-AP_run-01_dwi.bvec /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir98/sub-MDP001_acq-98_dir-PA_run-01_dwi.bvec > /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_PA_dir98.bvec
+
+paste -d ' ' /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-AP_run-01_dwi.bvec /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/raw/dir99/sub-MDP001_acq-99_dir-PA_run-01_dwi.bvec > /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/AP_PA_dir99.bvec
+
+# Run eddy on dir98 and dir99 scans
+eddy_openmp --imain=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_raw --mask=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0_brain_mask --acqp=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/acqparams.txt --index=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/index.txt --bvecs=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_PA_dir98.bvec --bvals=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_PA_dir98.bval --topup=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/topup_AP_PA_b0 --out=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_raw --flm=quadratic
+
+eddy_openmp --imain=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/sub-MDP001-AP_PA_dir99_raw --mask=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0_brain_mask --acqp=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/acqparams.txt --index=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/index.txt --bvecs=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/AP_PA_dir99.bvec --bvals=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/AP_PA_dir99.bval --topup=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/topup_AP_PA_b0 --out=/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/sub-MDP001-AP_PA_dir99_raw --flm=quadratic
+
--- a/example-bash-scripts/sub-MDP001-reg.sh
+++ b/example-bash-scripts/sub-MDP001-reg.sh
+#!/bin/bash
+#SBATCH --partition=express
+#SBATCH --time=2:00:00
+#SBATCH --ntasks=1
+#SBATCH --mem-per-cpu=8G
+#SBATCH --output=/data/user/mdefende/datasets/MDP-diff/jobs/register/sub-MDP001-reg.txt
+
+module load FreeSurfer/6.0.0-centos6_x86_64
+SUBJECTS_DIR=/data/user/mdefende/datasets/MDP/subs
+
+bbregister --s sub-MDP001 --mov /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0.nii.gz --dti --reg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --init-fsl
+
+bbregister --s sub-MDP001 --mov /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0.nii.gz --dti --reg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --init-fsl
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.1e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir98_diff_1.1e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.1e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir98_diff_1.1e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.6e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir98_diff_1.6e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.6e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir98_diff_1.6e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.1e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir99_diff_1.1e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.1e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir99_diff_1.1e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.6e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir99_diff_1.6e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.6e-9_odi.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir99_diff_1.6e-9_odi.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.1e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir98_diff_1.1e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.1e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir98_diff_1.1e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.6e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir98_diff_1.6e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir98/sub-MDP001_diff_1.6e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir98_diff_1.6e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir98_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.1e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir99_diff_1.1e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.1e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir99_diff_1.1e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi rh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.6e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/lh.sub-MDP001_dir99_diff_1.6e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi lh
+
+mri_vol2surf --src /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/NODDI/dir99/sub-MDP001_diff_1.6e-9_ficvf.nii --out /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/rh.sub-MDP001_dir99_diff_1.6e-9_ficvf.mgz --srcreg /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/register/dir99_reg.dat --hemi rh
--- a/example-bash-scripts/sub-MDP001_dir98_1.1e-9.sh
+++ b/example-bash-scripts/sub-MDP001_dir98_1.1e-9.sh
+#!/bin/bash
+#SBATCH --partition=long
+#SBATCH --time=72:00:00
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=8
+#SBATCH --mem-per-cpu=8G
+#SBATCH --output=/data/user/mdefende/datasets/MDP-diff/jobs/noddi/sub-MDP001_dir98_1.1e-9.txt
+
+module load rc/matlab/R2019a
+module load FreeSurfer/6.0.0-centos6_x86_64
+
+mri_convert /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_eddy.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_eddy -ot nifti1
+
+mri_convert /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0_brain_mask.nii.gz /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0_brain_mask -ot nifti1
+
+matlab -nodisplay -r "addpath(genpath('/data/user/mdefende/Projects/prl-noddi/code'));CreateROI('/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_eddy.hdr','/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0_brain_mask.hdr','/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_eddy_NODDI_roi.mat');protocol = FSL2Protocol('/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/AP_PA_dir98.bval','/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_eddy.eddy_rotated_bvecs',5);noddi = MakeModel('WatsonSHStickTortIsoV_B0',1.1e-9); batch_fitting('/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/sub-MDP001-AP_PA_dir98_eddy_NODDI_roi.mat',protocol,noddi,'/data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/NODDI_fitted_params_diff_1.1e-9.mat',8);"