Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you!
1) MG93 2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer!
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.3.1.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/MG93_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
The CT itself has incorrect parameters for the pixel size. You can try using 9 dof instead of 6, but in the end you'll want to fix your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you!
- MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer!
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.3.1.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/MG93_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Are any of the CT scans for this patient okay? How can I check? The one I picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to? ________________________________________ 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: Friday, November 20, 2015 12:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sheered CT in tkregister2
The CT itself has incorrect parameters for the pixel size. You can try using 9 dof instead of 6, but in the end you'll want to fix your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you!
- MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer!
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.3.1.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/MG93_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
look at them in freeview 9 dof means 9 degrees of freedom in the registration, 3 translation, 3 rotation, and 3 scale. The 3 scale may account for errors in the voxels size of the ct
On 11/20/2015 12:54 PM, Borzello, Mia wrote:
Are any of the CT scans for this patient okay? How can I check? The one I picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to? ________________________________________ 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: Friday, November 20, 2015 12:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sheered CT in tkregister2
The CT itself has incorrect parameters for the pixel size. You can try using 9 dof instead of 6, but in the end you'll want to fix your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you!
- MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer!
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.3.1.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/MG93_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is there a way to change the scale in freeview?
Thanks, Mia ________________________________________ 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: Friday, November 20, 2015 1:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sheered CT in tkregister2
look at them in freeview 9 dof means 9 degrees of freedom in the registration, 3 translation, 3 rotation, and 3 scale. The 3 scale may account for errors in the voxels size of the ct
On 11/20/2015 12:54 PM, Borzello, Mia wrote:
Are any of the CT scans for this patient okay? How can I check? The one I picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to? ________________________________________ 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: Friday, November 20, 2015 12:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sheered CT in tkregister2
The CT itself has incorrect parameters for the pixel size. You can try using 9 dof instead of 6, but in the end you'll want to fix your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you!
- MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer!
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.3.1.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/MG93_SurferOutput/mri
ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
not that I know of (Ruopeng can chime in). You can use mri_convert to change the voxel size using the -ois, -ojs, or -oks flags. You'll have to experiment to see which done and what the value needs to be
On 11/22/2015 04:59 PM, Borzello, Mia wrote:
Is there a way to change the scale in freeview?
Thanks, Mia ________________________________________ 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: Friday, November 20, 2015 1:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sheered CT in tkregister2
look at them in freeview 9 dof means 9 degrees of freedom in the registration, 3 translation, 3 rotation, and 3 scale. The 3 scale may account for errors in the voxels size of the ct
On 11/20/2015 12:54 PM, Borzello, Mia wrote:
Are any of the CT scans for this patient okay? How can I check? The one I picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to? ________________________________________ 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: Friday, November 20, 2015 12:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] sheered CT in tkregister2
The CT itself has incorrect parameters for the pixel size. You can try using 9 dof instead of 6, but in the end you'll want to fix your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you!
- MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer!
RedHat release: CentOS release 6.7 (Final)
Kernel info: Linux 2.6.32-573.3.1.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/MG93_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Borzello, Mia -
Douglas N Greve