om: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl
Sent: Friday, April 13, 2007 4:56 PM
To: Derin Cobia
Cc: [EMAIL PROTECTED]
Subject: Re: [Freesurfer] bad white surface
I see. 1x1x1 with standard coils is pretty noisy at 1.5T. That's why we
used to use 1.3x1.3x1 instead,
I see. 1x1x1 with standard coils is pretty noisy at 1.5T. That's why we
used to use 1.3x1.3x1 instead, although now we do 1mm is at 3T with a 12
or 32 channel. Sorry, it's hard to describe what to fix since it depends on
exactly what happened. You have to find what string of wm voxels in the
wm
Thanks Nick. I am familiar with those pages, but none of those defects
are apparent in this subject (e.g., no misclassifications, lesions, or
failure to have the ventricles filled). The surface just appears to jump
from one section to another over blank space (or over gm in the
brainmask.mgz volu
What should I erase? Sorry, I did mean to say I saw the surface errors
overlaid on the volume, but couldn't discern any in the wm.mgz alone.
It's 3D FLASH on a Vision 1.5T, TR/TE= 20/5.4 ms, flip=30 deg, 1
acquisition, 1x1x1 mm^3 voxels. Nothing fancy, maybe that's the
problem...
-Derin
> it l
Derin,
The tutorial pages showing which defects to look for and how to fix them
start here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
this includes white matter edits:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
Nick
On Fri, 2007-04-13
it looks like there is an (incorrect) connection in the wm.mgz from the
temporal lobe across the insula. The data also looks really noisy - what
is the acquisition? You'll need to erase some stuff form the wm.mgz I
think.
On Fri, 13 Apr 2007, Derin Cobia wrote:
Here is a pic of the inflated.
look at the ?h.inflated.nofix to see what is causing the defect, and
correct the wm.mgz manually to remove it. Jenni: can you point Derin at the
appropriate wiki page?
thanks,
Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundar
The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary
appropriately. What should I try next?
-Derin
> this is probably a topology fixing problem. Look at the ?h.orig.nofix and
> see how it is
> On Fri, 13 Apr 2007, Derin Cobia wrote:
>
>> Did you mean wm.mgz? It looks fine. Th
this is probably a topology fixing problem. Look at the ?h.orig.nofix and
see how it is
On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either.
Here's a pic.
-Derin
Hi Derin,
What does the orig surface look like? and the wm? Are
Hi Derin,
What does the orig surface look like? and the wm? Are those correct?
Jenni
On Fri, 13 Apr 2007, Derin Cobia wrote:
I have two subjects where the white surface does not follow the gray-white
gradient (see attached pic for example). Is there any way to fix this?
I'm assuming it has
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