TBSS - Tract-Based Spatial Statistics

Proposed Workflow

Assuming this type of directory structure

- Study1
 - data
 - scripts

'Study1' is the folder containing all your datafiles and scripts. 'data' contains the mri data files. TBSS has four basic steps,

1. tbss_1_preproc
2. tbss_2_reg
3. tbss_3_postreg
4. tbss_4_prestats
5. stats (randomise etc...)

Step 1 - tbss_1_preproc

We first create a slurm submission script (located in the scripts directory)

Contents of dti-part1.sh:

#!/bin/sh
#SBATCH -n 1           # 1 cores
#SBATCH -t 1:00:00     # 1 hour
#SBATCH -p compute      # partition name
#SBATCH -U thpsy   # your project name - contact Ops if unsure what this is
#SBATCH -J TBSS18_18  # sensible name for the job

cd ../data

echo "################################################################################"
echo "### tbss preprocessing"
tbss_1_preproc *.nii.gz

We then submit this script to the queue system.

sbatch dti-part1.sh

Step 1 should not take too long.

Step 2 - tbss_2_reg

We then create another slurm script, again located in the scripts directory.

Contents of dti-part2.sh:

#!/bin/sh
#SBATCH -n 1           # 1 cores
#SBATCH -t 1:00:00     # 1 hour
#SBATCH -p compute      # partition name
#SBATCH -U thpsy   # your project name - contact Ops if unsure what this is
#SBATCH -J TBSS18_18  # sensible name for the job

cd ../data

echo "################################################################################"
echo "### tbss step 2 (registration using study specific template)"
tbss_2_reg -n

This script should only be run when Step 1 is completed.

We then submit this script to the queue system:

sbatch dti-part2.sh

This step usually takes the longest. The tbss_2_reg script uses a modified version of the 'fsl_sub' script to take advantage of the queuing system. It will automatically submit all the sub-tasks to the queue system. This may be in the order of thousands of jobs depending on the size of your study.

You must wait for *all* the jobs to complete before moving onto the next step. You can check the status of your jobs by doing the following

squeue -u USERNAME -l

where USERNAME is your own username on the clusters.

Step 3 - tbss_3_postreg and tbss_4_prestats

Once all the jobs from Step 2 has completed, prepare the following script (again located in your scripts directory) You may want to separate these two steps if you have a large study.

Contents of dti-part3.sh:

#!/bin/sh
#SBATCH -n 1           # 1 cores
#SBATCH -t 1:00:00     # 1 hour
#SBATCH -p compute      # partition name
#SBATCH -U thpsy   # your project name - contact Ops if unsure what this is
#SBATCH -J TBSS18_18  # sensible name for the job

cd ../data

echo "################################################################################"
echo "### tbss step 3 (post registration)"
tbss_3_postreg -S

echo "########################################################################"
echo "### tbss step 4 (scaling)"
tbss_4_prestats 0.2

Submit the jobs:

sbatch dti-part3.sh

Step 4 - Stats

Once all the above has been done, you can do the following (or something similar) in the stats directory.

design_ttest2 design 18 18 -n
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 -x --T2 -V

Or you can submit it to the queue system by creating the following slurm script in your scripts directory:

#!/bin/sh
#SBATCH -n 1           # 1 cores
#SBATCH -t 1:00:00     # 1 hour
#SBATCH -p compute      # partition name
#SBATCH -U thpsy   # your project name - contact Ops if unsure what this is
#SBATCH -J TBSS18_18  # sensible name for the job

cd ../data/stats
design_ttest2 design 18 18 -n
randomise_parallel -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 -x --T2 -V

We then submit this script to the queue system:

sbatch dti-part4.sh

If you are running randomise_parallel, you will need to run ./tbss.defragment once all the sub-jobs are completed to recombine the data.

To view the results, go into the stats directory and run the following commands:

tbss_fill tbss_tfce_corrp_tstat1 0.95 mean_FA tbss_fill
fslview mean_FA -b 0,0.6 mean_FA_skeleton -l Green -b 0.2,0.7 tbss_fill -l Red-Yellow

It is best to refer back to the original TBSS pages for how to use these programs, http://www.fmrib.ox.ac.uk/fsl/tbss/index.html