Hi Gabriel,
Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt.
The surfaces will be saved in a subdirectory called "ascii" inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension.
Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate.
Hope it helps!
All the best,
Anderson
On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:
Hello all FS users and experts,
I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands:
First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space
Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh
And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc
I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first...
Many Thanks in advanced, Gabriel
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Hi Gabriel,
This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and its explicit use only makes a difference for Mac users, who have to get it from MacPorts or Fink.
Also, the first script should work with bash. The sh can be ash, dash or even other depending on the system, being all with less features than bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may work with any, but this isn't always the case.
All the best!
Anderson
On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote:
Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it. Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time: [root@localhost] srf2obj aseg_004.srf > aseg_4.obj gawk: /root/freesurfer/bin/srf2obj:2: ' invalid on the expressionrfer/bin/srf2obj:2: ^ character '
Regards, Gabriel
El 07/05/12, *Anderson Winkler * andersonwinkler@hotmail.com escribió:
Hi Gabriel,
Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt.
The surfaces will be saved in a subdirectory called "ascii" inside each subject's directory, and have extension .srf. They are internally the same as the .asc surfaces, just with a different extension.
Note that the idea of the script is to generate surfaces for visualization purposes only. If you'd like to do statistical analysis (e.g., compare shapes between patients and controls), these surfaces may not be appropriate.
Hope it helps!
All the best,
Anderson
On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:
Hello all FS users and experts,
I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file, For this I'm using the next commands:
First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii To preserve the aseg volume in native space
Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mgh
And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc
I'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first...
Many Thanks in advanced, Gabriel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Anderson Winkler -
Gabriel Gonzalez Escamilla