That looks pretty good to me considering the resolution and 7T. We will
be re-evaluating the hires stream over the next year. If you want to
contribute a problem data set to our test suite, that would be appreciated.
doug
On 4/17/17 1:45 PM, Damien MARIE wrote:
Hi,
I have a project on 7T data. I processed 26 subjects with FreeSurfer6
recon-all with or without the hires flag. The input is MP2RAGE, 0.6
mm^3, bias corrected, skull strip was done despite a slight piece of
dura is still present.
For the data processed at native resolution, with the hires flag, I
mainly used this: recon-all -subject -i -parallel -expert -hires
The expert file indicating only mris_inflate -n 50
As a result, skull strip had to be fixed for 5 subjects (missing brain
pieces). Bilateral temporal pole is missing in the reconstructed
surfaces in 19 subjects.
For the downsampled data, without the hires flag : recon-all -subject
-i -parallel
Bilateral temporal pole is missing in the reconstructed surfaces in
only 1 subject. Surfaces are way smoother.
I guess such differences between the classic pipeline and the pipeline
tuned for hires data are expected.
I was just wondering if I was missing something somewhere, some
additional options that I would need to tweak, to get better surfaces
with the hires data especially in the temporal pole. For now the only
things I see that I could do are adding checkpoints or play with this
command line: mris_make_surfaces -max_gray_at_csf_border X -max_csf Y
Thank you and best,
*Damien*
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