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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 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; '''1- Applescript''' It works using 4 mouse clicks onlyt! |
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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.zip|freesurferstats2table]] [[http://youtu.be/o7uX70xstws|The illustration video]] '''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; | |
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| This script is suitable for MAC only. | |
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| '''For aseg.stats and wmparc.stats''' | |
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| asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt | '''2- Bash script''' |
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| '''For ?h.aparc.stats ''' | |
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| aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt | |
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| '''For ?h.aparc.2009s.stats ''' | '''aseg.stats and wmparc.stats''' |
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| aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt | asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt |
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| '''For'''''' ''''''?h.BA.stats''' | '''?h.aparc.stats''' |
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| aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt | aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt '''?h.aparc.2009s.stats''' aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt '''?h.BA.stats''' aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt |
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 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;
1- Applescript
It works using 4 mouse clicks onlyt!
Please click on the link below to download script;
freesurferstats2table The illustration video This script is suitable for MAC only.
2- Bash script
aseg.stats and wmparc.stats
asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt
?h.aparc.stats
aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt
?h.aparc.2009s.stats
aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt
?h.BA.stats
aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt