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Easyfreesurfer is a simple script which was written to simplify and automate most freesurfer processes. It controls some commands such as; recon-all and mri_convert without writing any command in terminal, hence user will only need to use mouse to select options and click buttons. Two scripts have been written, one works on Mac OS X and Linux '''(bash script)'''. The other is an applescript which works with both shell types '''''bash'' and '''''tcsh'' but it is suitable for '''''Mac OS X'' only . Easyfreesurfer is a simple script which was written to simplify and automate most freesurfer processes. It controls some commands such as; recon-all and mri_convert without writing any command in terminal, hence user will only need to use mouse to select options and click buttons.
Two scripts have been written, first one is '''applescript''' which works with both shell types '''bash''' and '''tcsh''' but it is suitable for '''Mac OS X''' only. The other one is a '''(bash script)''' that works on Mac OS X and Linux.

'''1- Applescript'''

Please click on the link below to download script:

[[http://www.nitrc.org/frs/download.php/4342/Easy_Freesurfer.zip|Easy_Freesurfer]]

[[attachment:easyfreesurfer_help.pdf]]
[[http://www.youtube.com/watch?v=EY8beEgrhVk|The illustration video]]


    '''multi mri_convert'''

Please click on the link below to download script:

[[attachment:Multiple mri_convert.zip]]
[[http://www.youtube.com/watch?v=c5EiDUTKOdI|The illustration video]]


'''***********************************************************************************************************'''

'''2- Bash script'''
Please click on the link below to download script:

[[http://www.nitrc.org/frs/download.php/4669/easyfreesurfer_bash.zip|Easy_Freesurfer_bash]]

For using this script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there.
Bash script works on bash shell only where "chmod +x" command used to make it executable as following;

chmod +x easyfreesurfer_bash.command

or

chmod +x easyfreesurfer_bash.sh

Easyfreesurfer is a simple script which was written to simplify and automate most freesurfer processes. It controls some commands such as; recon-all and mri_convert without writing any command in terminal, hence user will only need to use mouse to select options and click buttons. Two scripts have been written, first one is applescript which works with both shell types bash and tcsh but it is suitable for Mac OS X only. The other one is a (bash script) that works on Mac OS X and Linux.

1- Applescript

Please click on the link below to download script:

Easy_Freesurfer

easyfreesurfer_help.pdf The illustration video

  • multi mri_convert

Please click on the link below to download script:

Multiple mri_convert.zip The illustration video

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

2- Bash script Please click on the link below to download script:

Easy_Freesurfer_bash

For using this script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there. Bash script works on bash shell only where "chmod +x" command used to make it executable as following;

chmod +x easyfreesurfer_bash.command

or

chmod +x easyfreesurfer_bash.sh

Easyfreesurfer (last edited 2012-06-04 20:14:12 by 2)