Hi, no problem. I used the command "mri_convert" but I just checked the slice thickness on it, and it's has a thickness of 2. So that's probably the problem then? Sorry for all the issues, I thought this CT would work.
Thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 20, 2014 6:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] skewed CT viewed in tkregister2
Hi Mia, sorry for the delay. I think the problem is that the geometry info in the CT header is incorrect. The directions are not orgthogonal, and, when made orthogonal, the pixel sizes look wrong. How did you create ct.mgz?
doug
On 10/12/2014 08:52 PM, Borzello, Mia wrote:
Hi,
Any insight on this problem I'm having with tkregister2? I haven't been able to resolve this yet. My original posting is below with the output from bugr.
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, October 06, 2014 11:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] skewed CT viewed in tkregister2
Hi Freesurfers
I'm having trouble viewing a CT in tkregister2. Here is the output from bugr:
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
PWD: /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri
- BI20
- tkregister2 --s BI20v2_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig
- the coronal/saggital/horizontal views were skewed
4.attached.
Thanks a lot, Mia
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