|
Size: 1192
Comment:
|
Size: 1536
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| 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! | The following scripts 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 those scripts will simplify and automate conversion process. '''1- Applescript''' It works using 4 mouse clicks only!''' This script works on both bash and tsch shells but it is suitable for MAC only.''' |
| Line 4: | Line 9: |
| freesurferstats2table | [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2011/3/10_freesurfer_stats2table_(asegstats2table_and_aparcstats2table)_files/freesurferstats2table.zip|freesurferstats2table_applescript]] |
| Line 6: | Line 11: |
| [[http://youtu.be/o7uX70xstws|The illustration video]] | |
| Line 7: | Line 13: |
| This script is suitable for MAC only. | '''***********************************************************************************************************''' |
| Line 9: | Line 15: |
| 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; | '''2- Bash script''' |
| Line 11: | Line 17: |
| For aseg.stats and wmparc.stats asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt |
'''This script works on both Linux and MAC.''' But it works on bash shell only. |
| Line 14: | Line 19: |
| For ?h.aparc.stats aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt |
User will be asked to write freesurfer directory and subjects' directory. |
| Line 17: | Line 21: |
| For ?h.aparc.2009s.stats aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt |
You can use '''chmod +x''' to make it executable as following; |
| Line 20: | Line 23: |
| For ?h.BA.stats aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt |
chmod +x stats2table_bash.command '''or''' chmod +x stats2table_bash.sh Please click on the link below to download script; [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2010/12/23_Bash_scripting_and_freesurfer_(2)_files/freesurferstats2table_bash.zip |freesurferstats2table_bash]] [[http://youtu.be/_D2UbT-1mY0|The illustration video]] ---- CategoryHomepage CategoryCategory CategoryCategory |
The following scripts 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 those scripts will simplify and automate conversion process.
1- Applescript
It works using 4 mouse clicks only! This script works on both bash and tsch shells but it is suitable for MAC only.
Please click on the link below to download script;
freesurferstats2table_applescript
***********************************************************************************************************
2- Bash script
This script works on both Linux and MAC. But it works on bash shell only.
User will be asked to write freesurfer directory and subjects' directory.
You can use chmod +x to make it executable as following;
chmod +x stats2table_bash.command or chmod +x stats2table_bash.sh
Please click on the link below to download script;