Sunday, 20 March 2011

Create an averaged brain in Brainvoyager QX


Regional differences in sulcal and gyral topography can be used as disease indications such as in schizophrenia (Csernansky et al., 2008). In the previous video I showed how we can combine multiple aligned surfaces (.srf files) in one surface brain like the following image;

For combining multiple volumes (.vmr files), we use another function in BrainVoyager QX. This function can be accessed in two ways;
1- Through Volumes tab and mouse click on Combine 3D Data Sets... sub tab as shown in the following image.

2- By clicking on 3D Volume Tool then selecting Talairach tab then clicking Combine Data Sets... button as shown in the following image.


After selecting one of the previous options we will get window like the following one, we select wanted files and press on Average button.
The resulted average looks like the following image;

Related links
Run multiple BrainVoyager instances on Mac OSX

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.





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.



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

Tuesday, 8 March 2011

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;


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

or

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

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