Diff for "freesurferstats2table"

Differences between revisions 7 and 33 (spanning 26 versions)

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;

freesurferstats2table

The illustration video

***********************************************************************************************************

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. Both directories can be dragged in terminal window

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

-  ⇤ ← Revision 7 as of 2011-07-07 21:06:58 → 
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+   ← Revision 33 as of 2011-07-09 13:09:26 → ⇥
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  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 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;

'''1- Applescript''' 

It works using 4 mouse clicks only!'''  This script is suitable for MAC only.'''
-Line 5:
+Line 9:
-  [[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]]
-Line 7:
+Line 11:
+[[http://youtu.be/o7uX70xstws|The illustration video]]
-Line 8:
+Line 13:
-This script is suitable for MAC only.
+'''***********************************************************************************************************'''

'''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. '''Both directories can be dragged in terminal window'''  

Please click on the link below to download script;
-Line 12:
+Line 25:
-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;
-Line 15:
+Line 27:
-  '''For aseg.stats and wmparc.stats'''
-Line 17:
+Line 28:
- asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt
-Line 19:
+Line 29:
-  '''For ?h.aparc.stats '''
+'''aseg.stats and wmparc.stats'''
-Line 21:
+Line 31:
- aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt
+asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt
-Line 23:
+Line 33:
-  '''For ?h.aparc.2009s.stats '''
+'''?h.aparc.stats'''
-Line 25:
+Line 35:
- aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt
+aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt
-Line 27:
+Line 37:
-  '''For'''''' ''''''?h.BA.stats'''
+'''?h.aparc.2009s.stats'''
 
aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc aparc.a2009s --meas volume --tablefile lh.aparc.a2009s.volume.txt
-Line 29:
+Line 41:
- aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt
+'''?h.BA.stats'''

aparcstats2table --hemi lh --subjects bert ernie fred margaret -- parc BA --meas volume --tablefile lh.BA.volume.txt