this looks like your brain mask contains bright dura mater
that gets mis-classified as white matter, this I assumed
happened n the skull stripping step, If you edit the brain mask
to exclude the offending dura you should be fine (or
alternatively it might help to edit the wm.mgz so the voxels
contain a value of 1 where the offending dura sits, but I am not
sure that this will work) and then re-run the following steps of
the recon. So have a look at brainmask.mgz. I assume with image
you mean volume? I believe this really is showing that you
might need to play with the skull-stripping process a bit to get
rid of the sure better (or with your sequence so you get less
signal from those structures in the first place ;) )
Best Regards
Sebastian
On Aug 26, 2014, at 13:50 , Melanie Ganz <Melanie.Ganz@nru.dk> wrote:
Dear Freesurfer community,
We've encountered a strange situation where the pial and wm surface delineation is successful for one image but contains wm (and subsequent pial) errors for another, almost identical structural image (see attached image, red and yellow are for the successful surface and blue and green are for the failed one). We've tried to identify the source for this discrepancy but I'm at a loss. All voxels of the original input images are identical to the 4th decimal and when converted to orig.mgz only a few voxels appear to be different due to rounding, none of which overlap with the wm surface errors. Both images were processed on the same setup (hardware and software, Freesurfer stable 5.3). Unfortunately, this error is quite systematic in my dataset; about 10% of the images show this type of error. Any suggestions on how to investigate this? I've uploaded example of good and bad at recon ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming/failed_wm_recon.tar.gz in case you'd like to have a closer look.
Thanks for your help.
Vincent and Melanie
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