Software at CIS : lddmm-volume : FAQ

Here are answers to some common questions you might have. If you have question other than thats listed here, please go to the feedback section to let us know. We will keep this page updated based on the questions users will have.

Technical:

What input formats does the LDDMM work with?
Both the template image and the target image has to be in the Analyze 7.5 format. For more information on the Analyze software from the Mayo foundation click here.
How can the output be visualized?
The output currently cannot be directly visualized as it only comprises of the Velocity Maps and the Diffiomorphisms. But after some conversion it can be visualized using MayaVi, ParaView or Slicer.
What kind of hardware, operating systems does the tool run on?
LDDMM currently runs on AIX 4 on a IBM RS/6000 SP, as well as on ItaniumII under linux. LDDMM has also runs on x86_64 architecture.

General

How can I download the software?
The software is not available to download currently.
How is the software being used currently?
LDDMM currently is being used in conjunction with data from MGH to do image analysis and matching.
The tutorial Statistical Computation and Inference on the Subcortical Surface: Search for Biomarkers in Neuropsychiatry illustrates the use of LDDMM in a project studying the human hippocampus.
Are there any future plans to this project?
Yes! LDDMM is slated to be a major part of the BIRN project. LDDMM will run in a decentralized manner and will process data from various partner institutions across the country. This again will adhere to the Single Program Multiple Data (SPMD) architecture.
How do I use this tool on the CIS cluster?
Users who have accounts at CIS can run lddmm jobs on the CIS cluster. In the following the text USER should be replaced by your CIS account name. The following example runs lddmm on images stored in a directory named morosdemo under USER home directory. Download Deforming Sphere Input from Calibration section. Unzip files and copy to morosdemo directory. To copy using secure copy (scp):
```
scp Ball3* [email protected]:/cis/home/USER/morosdemo/.
```
Download PBS Script and copy to morosdemo directory. Edit the pbsScript file, substituting CIS acount name for USER. Run the script by logging on to the CIS cluster (named moros) and submitting the pbsScript using the following commands
```
ssh foo.cis.jhu.edu
ssh moros
cd morosdemo
qsub pbsScript
```
This will submit the script to the pbs queue. This example takes approximately twelve minutes to run. To check on progress submit command
```
qstat
```
The above example uses the default parameters for lddmm. To modify paramters, download LDDMM Configuration Template from manual section. Copy this file to morosdemo directory. Rename file to lddmm.conf and enter parameters. Edit change last line of pbsScript from
```
lddmm -A Ball3D_1.img -T Ball3D_2.img
```
to
```
lddmm -c lddmm.conf
```
Submit pbsScript to qsub as above.
How can I contact the author of the tool?
Please refer to the feedback section.

Last Modified: Thursday, 30th May, 2013 @ 09:26am