ok, just posted... please, see here: http://brainder.org
On 08/05/12 15:51, Anderson Winkler wrote:
Hi Gabriel,
Please, try downloading from here:
http://dl.dropbox.com/u/2785709/aseg2srf
http://dl.dropbox.com/u/2785709/srf2obj
Right-click and click Save As, to avoid Windows opening it up and
messing up with character encoding. I'll write up a page about the
aseg2srf and send the link later...
All the best,
Anderson
On 08/05/12 14:31, Gabriel Gonzalez Escamilla wrote:
Anderson,
I'm downloading using a windows computer (but I always do like that
with every single script), which automatically recognizes the scripts
as txt files and add the extension, could you send me a link to the
downloading page? That way I can try again and see what happens. I
did check in my Linux distribution and is just as you said, the gawk
is the default, so I have no any other idea for this.
Regards,
Gabriel
El 08/05/12, *Anderson Winkler * <andersonwink...@hotmail.com> escribió:
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 * <andersonwink...@hotmail.com>
<andersonwink...@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
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Laboratory of Functional Neuroscience
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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/
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