On Sat, 2009-10-10 at 21:46 +0800, Angel Wong wrote:
> My version is 4.3.0. I will download the latest version and try again.
>
> Thank you.
>
> 2009/10/10 Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> I didn't do anything but run recon-all with the latest
> version. Remind me what version you were running?
>
>
> On Sat, 10 Oct 2009, Angel Wong wrote:
>
> Hi Bruce
>
> Thank you very much. The result looks much better than
> mine. How did you do
> that? Please let me know so that I can modify the
> other datasets if I face
> the same situation again.
>
> Cheers
> Angel
>
> 2009/10/10 Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
>
> Hi Angel,
>
> I'm just about done running the dataset and
> the results actually look ok
> (see attached tif). I didn't intervene at all,
> although you would want to to
> get rid of some non-brain tissue that the pial
> surface is grabbing, but
> that's pretty easy. Did you minimize your TE?
> I don't know what your
> gradient set is, but usually you can get your
> TE down a bit more than that.
> You also might be better off sacrificing a bit
> of resolution and lengthening
> your TR
> cheers,
> Bruce
>
>
> On Thu, 8 Oct 2009, Angel Wong wrote:
>
> Thanks a lot with your help. This is because
> we want to perform quite a
> number of functional runs on the same
> subject at the same session. So we
> tried to shorten the T1 scan time to
> minimize the motion artifacts come
> from
> the subject.
>
> Attached please find the orig.mgz for
> your information.
>
> 2009/10/8 Bruce Fischl
> <
fischl@nmr.mgh.harvard.edu>
>
> I see. Your TR is quite short and
> your TE relatively long, so this is
> probably pretty poor CNR
> between gray and white. If you
> send me the
> orig.mgz
> I'll take a look and see if
> it's fixable
>
> On Thu, 8 Oct 2009, Angel Wong
> wrote:
>
> Hi Bruce
>
>
> Attached please find
> the parameters for
> acquiring the T1
> image.
>
> Thank you for your
> help.
>
> Angel
>
> 2009/10/8 Bruce Fischl
> <
fischl@nmr.mgh.harvard.edu>
>
> eek, that looks
> pretty bad. Can you
> tell us what the
> acquisition
>
> parameters
> are?
>
> On Thu, 8 Oct
> 2009, Angel
> Wong wrote:
>
> Dear all
>
>
>
>
> Actually I would like to perform automated reconstruction for my T1
> image
> and
> then
> obtain
> anatomical labels after cortical parcellation. I have
> done
> fully
> automated reconstruction using recon-all. But for my case, the
> white
> and
> grey
> matter
> segmentation appears to be weird. The green line seems
> laying
> on the
> pial
> surface rather than on the white surface, and the
> red
> line
> seems
> including some non-brain structures (including small
> portion
> of
> CSF
> and
> skull). Thus, the resultant cortical thickness appears to be
> very
> thin
> after
> the
> segmentation. I just doubt if anything was going wrong
> during
> the
> procedure. Or need any preprocessing to enhance the segmentation
> quality
> before
> performing the reconstruction? If you have had similar
> situation
> as
> mine,
> please
> let me
> know
> how to
> tackle
> the
> problem.
>
> Attached please find the images for better illustration.
>
> fs_image_brain.tiff - use brain.mgz as aux volume
> fs_image_norm.tiff - use norm.mgz as aux volume
> fs_image_brainmask.tiff - use brainmask.mgz as aux volume and load
> segmentation file aseg.mgz
>
> Thanks
> Angel
>
>
>
>
>
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