Hello,
We ran into the following error during autorecon2 with one subject:
mri_fill: could not find any points where lh and rh wm are nbrs
It has been suggested to another user that the "-noaseg" flag be used. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06560.html) However, we would like to ask how this might affect the subsequent steps and how to take this into account in subsequent group analysis. Also, we would like to clarify if this would prevent the subcortical volumetric calculations.
Thanks! - Jerry
Jerry,
There was a problem in the recon-all script which you can fix. Edit recon-all, in the mri_fill section (look for --- Fill ---), on the line where it says 'if($UseAseg)', change 'aseg.mgz' to 'aseg.auto.mgz'.
The problem is that aseg.mgz contains the CC segmentations, and mri_fill is not aware of those segmentation labels (yet), so it doesnt find the CC. The aseg.auto.mgz is not CC-segmented, and mri_fill is able to find the CC. This fix will appears in the next release (v4.0.3).
Nick
On Mon, 2008-02-04 at 12:18 -0500, Jerry Yeou-Wei Chen wrote:
Hello,
We ran into the following error during autorecon2 with one subject:
mri_fill: could not find any points where lh and rh wm are nbrs
It has been suggested to another user that the "-noaseg" flag be used. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06560.html) However, we would like to ask how this might affect the subsequent steps and how to take this into account in subsequent group analysis. Also, we would like to clarify if this would prevent the subcortical volumetric calculations.
Thanks!
- Jerry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jerry,
what version of freesurfer are you using? And were you rerunning this subject, or was it the 1st time you ran it through? There was a bug with rerunning where the callosum would already be in the aseg and this would prevent us from finding the midline I think.
And yes, if you don't generate the aseg then you will have no subcortical volumes.
cheers, Bruce
On Mon, 4 Feb 2008, Jerry Yeou-Wei Chen wrote:
Hello,
We ran into the following error during autorecon2 with one subject:
mri_fill: could not find any points where lh and rh wm are nbrs
It has been suggested to another user that the "-noaseg" flag be used. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06560.html) However, we would like to ask how this might affect the subsequent steps and how to take this into account in subsequent group analysis. Also, we would like to clarify if this would prevent the subcortical volumetric calculations.
Thanks!
- Jerry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jerry Yeou-Wei Chen -
Nick Schmansky