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| 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.''' |
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| [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2011/3/10_freesurfer_stats2table_(asegstats2table_and_aparcstats2table)_files/freesurferstats2table.zip|freesurferstats2table]] | [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2011/3/10_freesurfer_stats2table_(asegstats2table_and_aparcstats2table)_files/freesurferstats2table_applescript.zip|freesurferstats2table_applescript]] |
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| [[http://youtu.be/o7uX70xstws|The illustration video]] | |
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| This script is suitable for MAC only. | '''***********************************************************************************************************''' |
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| 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''' |
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| '''This script works on both Linux and MAC.''' But it works on bash shell only. | |
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| '''For aseg.stats and wmparc.stats''' | User will be asked to write freesurfer directory and subjects' directory. |
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| asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt | You can use '''chmod +x''' to make it executable as following; |
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| '''For ?h.aparc.stats ''' | chmod +x stats2table_bash.command '''or''' chmod +x stats2table_bash.sh |
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| aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt | Please click on the link below to download script; |
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| '''For ?h.aparc.2009s.stats ''' | [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2010/12/23_Bash_scripting_and_freesurfer_(2)_files/freesurferstats2table_bash.zip |freesurferstats2table_bash]] |
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| aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt '''For'''''' ''''''?h.BA.stats''' aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt |
[[http://youtu.be/_D2UbT-1mY0|The illustration video]] ---- |
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
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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;