mri_convert_multidata

This script helps automate mri_convert command in freesurfer for large set of data 

For download
Multi_mri_convert

http://www.freesurfer.net/fswiki/Easyfreesurfer


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)

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

Easyfreesurfer

Easyfreesurfer is a simple script which was written to simplify and automate most freesurfer processes. It controls some commands such as; recon-all and mri_convert without writing any command in terminal, as user will only need to use mouse to select options and click buttons. This applescript works with both shell types bash and tcsh but it is suitable for Mac OS X only.

For download click here

http://www.freesurfer.net/fswiki/Easyfreesurfer

For using bash script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there. 

Bash script works on bash shell only where "chmod +x" command used to make it executable as following;

chmod +x easyfreesurfer_bash.command 

or

chmod +x easyfreesurfer_bash.sh

Easyfreesurfer_bash.zip

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

Related links

mri_convert_multidata

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

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

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)

Multiple directories creator

I’ve written this simple applescript to create multiple directories. An example of its use in neuroimaging is creating multiple subjects’ directories for freesurfer. In addition, there is an option to add subdirectories in each folder automatically like “mri/orig” in freesurfer. Those subdirectories are created using Terminal application, so you will see terminal application flashing because it will start and quit every 2 to 3 second during script running. It would create 100 folder within less than 10 seconds and up to 5 minutes for creating 100 folders with subdirectories. 

Multiple directories creator.zip

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