|
Size: 1431
Comment:
|
Size: 2224
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 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; |
| Line 3: | Line 3: |
| Please click on the link below to download script; | '''1- Applescript''' |
| Line 5: | Line 5: |
| [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2011/3/10_freesurfer_stats2table_(asegstats2table_and_aparcstats2table)_files/freesurferstats2table.zip|freesurferstats2table]] | It works using 4 mouse clicks only!''' This script is suitable for MAC only.''' |
| Line 7: | Line 7: |
| 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; | Please click on the link below to download script; |
| Line 9: | Line 9: |
| This script is suitable for MAC only. | [[http://web.me.com/jamaan/EASYNEUROIMAGING/Nuroimaging_blog/Entries/2011/3/10_freesurfer_stats2table_(asegstats2table_and_aparcstats2table)_files/freesurferstats2table.zip|freesurferstats2table]] |
| Line 11: | Line 11: |
| '''For aseg.stats and wmparc.stats''' | [[http://youtu.be/o7uX70xstws|The illustration video]] |
| Line 13: | Line 13: |
| asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt | '''***********************************************************************************************************''' |
| Line 15: | Line 15: |
| '''For ?h.aparc.stats ''' | |
| Line 17: | Line 20: |
| aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt | '''2- Bash script''' |
| Line 19: | Line 22: |
| '''For ?h.aparc.2009s.stats ''' | '''This script works on both Linux and MAC.''' but it works on bash shell only. |
| Line 21: | Line 24: |
| aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt | Please click on the link below to download script; |
| Line 23: | Line 26: |
| '''For'''''' ''''''?h.BA.stats''' | |
| Line 25: | Line 27: |
| aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt | |
| Line 27: | Line 28: |
'''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 |
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 only! This script is suitable for MAC only.
Please click on the link below to download script;
***********************************************************************************************************
2- Bash script
This script works on both Linux and MAC. but it works on bash shell only.
Please click on the link below to download 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