Hi Bruce,
I have attached the recon-all.log file for one of the subjects. By comparing the log file with other successful subjects, I can see some differences at the mri_edit_with_aseg:
Failed subject:
mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
MRIboundingBox: unsupported type 1
reading wm segmentation from wm.seg.mgz...
MRIboundingBox: unsupported type 1
auto filling took 1.68 minutes
0 voxels added to wm to prevent paths from MTL structures to cortex
0 additional wm voxels added
SEG EDIT: 0 voxels turned on, 1215 voxels turned off.
writing edited volume to wm.asegedit.mgz....
Succeeded subject:
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume...
auto filling took 1.03 minutes
reading wm segmentation from wm.seg.mgz...
515 voxels added to wm to prevent paths from MTL structures to cortex
2705 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 69225 voxels turned on, 29249 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 109 new 109
115,126,128 old 109 new 109
writing edited volume to wm.asegedit.mgz....
Zheng Hui
-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Thu 9/3/2009 11:25 PM
To: Zheng Hui
Cc: <Freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Wrong boundaries at ventricle.
Can you send us the recon-all.log?
On Sep 3, 2009, at 4:29 AM, "Zheng Hui" <zheng.hui@duke-nus.edu.sg>
wrote:
> Dear Bruce,
>
> In the attached image at the ventricle area, you can see the pial
> and white surfaces go into the ventricle, following the white/CSF
> boundary rather than going through the medial separation. And by
> looking at the wm.mgz, I can see the ventricles were not filled by
> the program although the ventricles were labelled correctly in
> aseg.mgz. Hope I describe the problem clearer this time. I have
> attached the image again.
>
> Thanks,
> Zheng Hui
>
> -------------------------------------------------------
> Hi Zheng,
>
> sorry, I don't see what you mean in the image. If you want to upload a
> dataset that has this problem I'll take a look.
>
> cheers,
> Bruce
> On Wed, 2 Sep 2009, Hui
> Zheng wrote:
>
> > Hi freesurfer,
> >
> > We are reprocessing our data from FS version 3.05 with the latest
> 4.50. We
> > found there are about 20% of the subjects have problem at the
> ventricle as
> > shown in the attached image. I have tried the method suggested by
> Doug to
> > remove the wm.mgz and rerun from autorecon2-cp. However, for two
> subjects I
> > have tried, the method did not help. It will be tedious to
> manually fill in
> > all the ventricles in wm.mgz. Any other work around?
> >
> > Thanks,
> > Zheng Hui
> >
> >
>
> <aseg.jpg>
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