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.niiTo 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.edu <Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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: ggon...@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.
