Wednesday 21 December 2011

Batching FSL tools and utilities using Applescript and bash script "2" (SIENAX)

This script has been written to automate and simplify SIENAX tool (FSL) without writing any command line. User only needs to specify data directory and to select options at the beginning. To download this script please click on the following link

I wrote a bash script to automate and simplify SIENAX tool. It works on both Linux and MAC, user needs to copy script to data directory and execute it from there. This script works on bash shell only where it can be executed using "chmod +x" command as following;

chmod +x sienax_bash.command or chmod +x
Bash script

SIENAX estimates total brain tissue volume, from a single image, normalised for skull size. It calls a series of FSL programs: It first strips non-brain tissue, and then uses the brain and skull images to estimate the scaling between the subject's image and standard space. It then runs tissue segmentation to estimate the volume of brain tissue, and multiplies this by the estimated scaling factor, to reduce head-size-related variability between subjects.

Please leave your feedback if you like this tool or a suggestion if you think it needs to be improved!

Related links

1 comment:

brocktoon said...

I am trying to run your script. I have my data set in both nii.gz format and hdr/img format. But when I open the script file, I am prompted with the error

"Missing hdr/img file." and "Failed to load base image. Command line processing aborted."

Can you please help me with these errors?