Dear all,
at the moment I am struggling with flattening monkey anatomical scans. Specifically I manually got to the point where I get a wm.mgz and now I want to inflate it. My instructions refer to using csurf, which does not like my mgz volumes and is deprecated IIRC, the alternative is hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing?
Ahoi & Thanks Sebastian
In the freesurfer dev releases post 2006-18-01, there is a -noaseg flag in recon-all. It will skip the auto-segmentation step, and not include aseg.mgz in any subsequent processing (eg. wm seg and filling). The flag is intended for usage with baby brains and non-human primates, as these brains cannot be auto-segmented with the default atlas (which is based on 40 adult normals).
On Wed, 2006-02-22 at 18:19 +0100, Sebastian Moeller wrote:
Dear all,
at the moment I am struggling with flattening monkey anatomical scans. Specifically I manually got to the point where I get a wm.mgz and now I want to inflate it. My instructions refer to using csurf, which does not like my mgz volumes and is deprecated IIRC, the alternative is hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing?
Ahoi & Thanks Sebastian
Hi Nick, hi All,
On 22. Feb 2006, at 19:39 Uhr, Nick Schmansky wrote:
In the freesurfer dev releases post 2006-18-01, there is a -noaseg flag in recon-all. It will skip the auto-segmentation step, and not include aseg.mgz in any subsequent processing (eg. wm seg and filling). The flag is intended for usage with baby brains and non-human primates, as these brains cannot be auto-segmented with the default atlas (which is based on 40 adult normals).
I still run the dev20051003 version, is everything else compatible? Anyway I used the -nofill directive for recon-all autorecon2-wm, after running mri_fill manually, supplying the required cc and pons coordinates, but specifying -noaseg sure beats my "do it by hand" approach, by far. Thanks for the impressive automatization work.
Ahoi & Thanks Sebastian
On Wed, 2006-02-22 at 18:19 +0100, Sebastian Moeller wrote:
Dear all,
at the moment I am struggling with flattening monkey anatomical scans. Specifically I manually got to the point where I get a wm.mgz and now I want to inflate it. My instructions refer to using csurf, which does not like my mgz volumes and is deprecated IIRC, the alternative is hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing?
Ahoi & Thanks Sebastian
Sebastian,
I've attached a gzipped recon-all that has the -noseg flag. Do not copy over the recon-all in your 2005-10-03 release, as it's not fully compatible with that. Rather, I suggest opening the new recon-all in a text editor, and look for instances of the variable 'UseAseg', and the - noaseg flag, and I think you can modify your existing recon-all to do the same. There is no magic involved, the -noaseg flag just does what you were probably doing manually. Your 2005-10-03 release should work with the changes.
Nick
On Wed, 2006-02-22 at 20:02 +0100, Sebastian Moeller wrote:
Hi Nick, hi All,
On 22. Feb 2006, at 19:39 Uhr, Nick Schmansky wrote:
In the freesurfer dev releases post 2006-18-01, there is a -noaseg flag in recon-all. It will skip the auto-segmentation step, and not include aseg.mgz in any subsequent processing (eg. wm seg and filling). The flag is intended for usage with baby brains and non-human primates, as these brains cannot be auto-segmented with the default atlas (which is based on 40 adult normals).
I still run the dev20051003 version, is everything else compatible? Anyway I used the -nofill directive for recon-all autorecon2-wm, after running mri_fill manually, supplying the required cc and pons coordinates, but specifying -noaseg sure beats my "do it by hand" approach, by far. Thanks for the impressive automatization work.
Ahoi & Thanks Sebastian
On Wed, 2006-02-22 at 18:19 +0100, Sebastian Moeller wrote:
Dear all,
at the moment I am struggling with flattening monkey anatomical scans. Specifically I manually got to the point where I get a wm.mgz and now I want to inflate it. My instructions refer to using csurf, which does not like my mgz volumes and is deprecated IIRC, the alternative is hooking my data into the recon-all pipe-line. But that fails as I do not have any aseg.mgz (does the segmentation work for monkeys?). So any advice on how to proceed with the processing?
Ahoi & Thanks Sebastian
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
Sebastian Moeller