glad to hear it
Bruce
On Mon, 6 Jul 2015, Clara Kühn wrote:
Hi Bruce,
it worked! The surfaces now look so much better.
Thanks for your help!
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 30. Juni 2015 17:18:26
Betreff: Re: [Freesurfer] too much white matter
Hi Bruce,
yes, it is an mp2rage image.
I'm gonna work in your suggestions and see if it changes anything after
rerunning the the recon-all process.
Thank you!
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 30. Juni 2015 16:18:06
Betreff: Re: [Freesurfer] too much white matter
Hi Clara
the second control point (135, 152, 163) is outside the brainmask. You will
need to correct the skull stripping first. In general I wouldn't put
control points in that type of location as it is certainly partial volumed.
I would try something like 139, 145, 163 instead (and maybe a couple around
there).
Also, I assume the skull stripping failed as this is not the typical type
of image we expect (since the background is so bright and noisy). Is it an
mp2rage or something? There appears to be very little space between skull
and brain so the stripping may be challenging, particularly in the
orbitofrontal region where you had this control point (it looks like fat is
shifting upwards either into or adjacent to brain)
cheers
Bruce
On Tue, 30 Jun 2015, Clara Kühn
wrote:
oh, and here are the Freesurfer coordinates for the control points:
86, 143, 147
135, 152, 163
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 30. Juni 2015 11:39:40
Betreff: Re: [Freesurfer] too much white matter
Hi Bruce,
thanks for your reply. As far as I can tell the cps are in the WM. I'd be
grateful if you could take a closer look, though. You can download the dataset
here:
https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Montag, 29. Juni 2015 18:07:28
Betreff: Re: [Freesurfer] too much white matter
Hi Clara
are you sure you put the control points in the interior of the WM? If you
want to upload the subject we will take a look
cheers
Bruce
On Mon, 29 Jun 2015, Clara
Kühn wrote:
Dear Freesurfer experts,
I've had this problem now a couple of times: after setting a few (in this case
2) control points and rerunning the recon-all process with the -cp flag I get
huge areas of white matter including the subcortical areas and lots of the
cortical ribbon. See attached picture.
Could you explain how this happens because the logfile says it ran without
error. In these cases I've deleted the whole thing and preprocessed the scan
from scratch. I was wondering if there's a better way to deal with this like
going a step back if that's possible.
Cheers,
Clara Kühn
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