I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and
try to draw control points I can see a little green cross about 1 voxel down
and to the right of the red cross, but as soon as I move the red cross they
vanish and I can no longer see them. FreeSurfer is saving the po
Upon further investigation it seems to be something wrong with my conversion
from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ
and the control points work fine. Has anyone had any issues converting between
mnc and mgz?
-Eric
-Original Message-
From: Faden
Hello-
I have just installed freesurfer. Although tksurfer and tkregister2 seem
to work fine, I get the following error message when attempting tkmedit:
X Error of failed request: BadRequest (invalid request code or no such
operation)
Major opcode of failed request: 129 (Apple-DRI)
Minor
Hi Nick-
Yes, I am. If tksurfer would still work on an Intel, then this appears
to be the problem. Will wait for a new release. Thanks.
Anthony
Nick Schmansky wrote:
Anthony,
Are you using a new Intel-processor based Mac? If so, we don't
support that just yet. The 'X Error' message is in
Anthony,
Are you using a new Intel-processor based Mac? If so, we don't support
that just yet. The 'X Error' message is indicative of this, I think.
The 'gcc' message can be ignored, it is an artifact of the FSL startup
script (included with the Freesurfer distribution).
Nick
On Tue, 1 A
what volume are you selecting them on? Make sure that it has been
"conformed" - that is, that it's 256^3 and 1mm isotropic.
On Tue, 1 Aug
2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and
try to draw control points I can see
can you give us details about how you did the conversion?
On Tue, 1 Aug
2006, Faden, Eric (NIH/NIMH) [F] wrote:
Upon further investigation it seems to be something wrong with my conversion
from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ
and the control points
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't.
Should I add blank slices to bring it to 256?
-Eric
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 8/1/2006 2:04 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.ed
mri_convert -c worked.
-Eric
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 8/1/2006 2:39 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Vanishing Control Points
no, you should use mri_convert -c to "conform" the
So my images come off the scanner as DICOM.
Steps For Both:
1) Convert DICOM to ANALYZE
2) Align and Average the scans
Steps For Broken:
3) Convert to minc to create a brain mask and do some normalization
4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing
monkeys)
5) U
no, you should use mri_convert -c to "conform" them. tkmedit is only
guaranteed to work with volumes that have been put through this process.
Bruce
On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH)
[F] wrote:
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't.
Should
If you're doing a recon, then there should be an mri/orig.mgz which is
conformed (ie, the dimension and voxel size will be 256^3 and 1mm^3)
regardless of what you start with. This is what you should be doing all
of your operations on (not necessarily orig.mgz, but a conformed
volume).
doug
Fa
I was wondering if setting the watershed parameters higher and
rerunning autorecon2 would expand the pial surface line if the outer
rim of the brain is being left out? Or would this not fix the problem?
Thanks
--
-Jake
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