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.

freesurferstats2table_bash.zip

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.

aparc2table_qdec.zip

http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table

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

Related links

Easyfreesurfer

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

mri_convert_multidata

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

This applescript can be used 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 using 4 mouse clicks!

Please click on the link below to download script;

freesurferstats2table

This script is suitable for MAC only.

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.

stats2table_qdec.zip

The main purpose of this script is to simplify and automate conversion process because subjects’ IDs should be written with some options in the command line depending on freesurfer stats file. So users will not need to write any thing when they use this script instead of command line;

asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt

http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table

or

aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt

http://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table

To visit script page in Freesurfer website please click on the following link 

http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table

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

Related links

Easyfreesurfer

mri_convert_multidata

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