Plastimatch is an application to perform registration of medical images such as X-Rays, CT, PET, and MRI..

References:

• Zaffino P, Raudaschl P, Fritscher K, Sharp GC, Spadea MF. Technical Note: plastimatch mabs, an open source tool for automatic image segmentation. Med Phys. 2016 Sep;43(9):5155.

• Plastimatch Main Site: Plastimatch

• Module Name: plastimatch (see the modules page for more information)
• Test data can be found in ${PLASTIMATCH_TEST_DATA}

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=4g
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 cn4224 are ready for job

[user@cn4224 ~]$ module load plastimatch
[user@cn4244 ~]$ cd /data/${USER}
[user@cn4224 ~]$ cp ${PLASTIMATCH_TEST_DATA}/* .
[user@cn4224 ~]$ tar xvzf registration-tutorial.tar.gz
[user@cn4224 ~]$ cd registration-tutorial
[user@cn4224 ~]$ plastimatch register parms.txt
Loading fixed image [0]: t5.mha
Loading moving image [0]: t0.mha
Launching registration worker thread
Inside registration worker thread
Doing registration stage
[1] xf_in->m_type = 0, xf_out->m_type = 0
RESAMPLE 0 1: (3 3 2), (3 3 2)
RESAMPLE 0 1: (3 3 2), (3 3 2)
volume_calc_grad complete.
plm_warp_native is complete.
[...]
Saving image...
Trying to write image to warped.mha
Load:   0.138638
Run:    1.27459
Save:   0.392006
Total:  1.80523
Finished!

Create a batch input file (e.g. plastimatch.sh) similar to the following.

#! /bin/bash

module load plastimatch
cd /data/${USER}
cp ${PLASTIMATCH_TESTDATA}/* .
tar xzf registration-tutorial.tar.gz
cd registration-tutorial
plastimatch register parms.txt

Submit these jobs using the Slurm sbatch command.

Create a swarmfile for the first step of the pipeline (e.g. plastimatch.swarm). For example:

plastimatch register parms_01.txt
plastimatch register parms_02.txt
plastimatch register parms_03.txt

Submit this job using the swarm command.

swarm -f plastimatch.swarm [-g #] --module plastimatch