TORTOISEV4 (Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble) is for processing diffusion MRI data.

References:

• C. Pierpaoli, L. Walker, M. O. Irfanoglu, A. Barnett, P. Basser, L-C. Chang, C. Koay, S. Pajevic, G. Rohde, J. Sarlls, and M. Wu, 2010,TORTOISE: an integrated software package for processing of diffusion MRI data, ISMRM 18th annual meeting, Stockholm, Sweden, #1597

Allocate an interactive session and run the program.
Sam ple session (user input in bold, example courtesy of M. Okan Irfanoglu, NIBIB):

[user@biowulf]$ sinteractive --cpus-per-task=32 --mem=32g --gres=gpu:v100:1
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load tortoisev4
[user@cn3144 ~]$ cd /data/${USER}
[user@cn3144 ~]$ TORTOISEProcess_cuda -u TESTSCAN/TESTSCAN_LR_DR.nii \
		     -d TESTSCAN/TESTSCAN_RL_DR.nii \
		     -s TESTSCAN/TESTSCAN_T2W_structural_weighted.nii.gz \
                     --gibbs 1 --gibbs_kspace_coverage 1  \
		     --rot_eddy_center  center_slice \
		     --repol 1 --s2v 1 --epi DRBUDDI

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. tortoisev4.sh). Example command below courtesy of M. Okan Irfanoglu (NIBIB):

#!/bin/bash
#SBATCH --cpus-per-task=32
#SBATCH --job-name=tortoisev4-test
#SBATCH --mem=32g
#SBATCH --time=12:00:00
#SBATCH --partition=gpu
#SBATCH --gres=gpu:v100:1

module load tortoisev4

cd /data/${USER}/

TORTOISEProcess_cuda -u TEST_SCAN/TEST_SCAN_LR_DR.nii \
                     -d TEST_SCAN/TEST_SCAN_RL_DR.nii \
                     -s TEST_SCAN/TEST_SCAN_T2W_structural_weighted.nii.gz \
                     --gibbs 1 \
                     --gibbs_kspace_coverage 1 \
                     --rot_eddy_center  center_slice \
                     --repol 1 \
                     --s2v 1 \
                     --epi DRBUDDI

Submit this job using the Slurm sbatch command.

sbatch tortoisev4.sh

Create a swarmfile (e.g. tortoisev4.swarm). For example:

TORTOISEProcess_cuda -u TEST_SCAN_01/TEST_SCAN_01_LR_DR.nii \
                     -d TEST_SCAN_01/TEST_SCAN_01_RL_DR.nii \
                     -s TEST_SCAN_01/TEST_SCAN_01_T2W_structural_weighted.nii.gz \
                     --gibbs 1 \
                     --gibbs_kspace_coverage 1 \
                     --rot_eddy_center  center_slice \
                     --repol 1 \
                     --s2v 1 \
                     --epi DRBUDDI
TORTOISEProcess_cuda -u TEST_SCAN_02/TEST_SCAN_02_LR_DR.nii \
                     -d TEST_SCAN_02/TEST_SCAN_02_RL_DR.nii \
                     -s TEST_SCAN_02/TEST_SCAN_02_T2W_structural_weighted.nii.gz \
                     --gibbs 1 \
                     --gibbs_kspace_coverage 1 \
                     --rot_eddy_center  center_slice \
                     --repol 1 \
                     --s2v 1 \
                     --epi DRBUDDI
TORTOISEProcess_cuda -u TEST_SCAN_03/TEST_SCAN_03_LR_DR.nii \
                     -d TEST_SCAN_03/TEST_SCAN_03_RL_DR.nii \
                     -s TEST_SCAN_03/TEST_SCAN_03_T2W_structural_weighted.nii.gz \
                     --gibbs 1 \
                     --gibbs_kspace_coverage 1 \
                     --rot_eddy_center  center_slice \
                     --repol 1 \
                     --s2v 1 \
                     --epi DRBUDDI

Submit this job using the swarm command.

swarm -f tortoisev4.swarm -g 32 -t 32 --partition gpu --gres=gpu:v100:1 --module tortoisev4