Tuesday 10 January 2012

Batching FSL tools and utilities using Applescript and bash script "4" (fslchfiletype) Analyze2Nifti--Nifti2Analyze

This script has been written to automate FSL utility (fslchfiletype). Using this script user could convert multiple images at once using a few mouse click. There are six options; 
Analyze (img) <---> Nifti (nii)
Analyze (img) <---> compressed Nifti (nii.gz)
Nifti (nii) <---> compressed Nifti (nii.gz)

To download this script please click on the following link nifti2analyze_applescript

I wrote a bash script to do the same job. 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 Analyze2Nifti-Nifti2Analyze.command or chmod +x Analyze2Nifti-Nifti2Analyze.sh

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

Related links


rtjohn1 said...

This is a great tool! Fslchfiletype is reliable and useful but sometimes, switching to a terminal, calling the script and specifying the input and output doesn't fit my work flow. With analyze2Nifti it's a call, two clicks and then you have a folder full of converted files.

Jamaan Alghamdi said...

Thank you very much Ryan for using this tool and commenting here. I appreciate your feedback.