Thursday 17 March 2011

Using bash script to convert freesurfer stats2table (asegstats2table & aparcstats2table)

At the previous entry, I presented how we can use applescript to control asegstats2table and aparcstats2table commands in order to generate text/ascii tables of freesurfer stats data for all subjects in the directory at once. At this entry I will show how we can write a bash script to control both asegstats2table and aparcstats2table commands. This bash script can be used in both Mac OS X and Linux.

The following script uses aparcstats2table and asegstats2table to extract cortical thickness, surface area and volume of manually defined regions of interest using stats files that resulted from qdec.

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

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1 comment:

WindStalker said...

Thanks. :) Really saved me the time to code all these up. Also, made me more confident of what I am doing lol. Cheers, mate. I'd buy you a beer/bottle if I meet you at HBM.