axial sheer

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Re: [Freesurfer] mri_vol2surf and...

Borzello, Mia

1 Jul 2012 1 Jul '12

9:58 p.m.

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

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axialPNG.PNG (image/png — 48.1 KB)

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Douglas Greve

1 Jul 1 Jul

11:28 p.m.

Can you give more info? Command line, description of data, where you got it from etc doug

On 7/1/12 9:58 PM, Borzello, Mia wrote:

...

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Borzello, Mia

2 Jul 2 Jul

10:05 a.m.

sure! at the command line: tkregister2 --s BWXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig this it's a CT of 124 slices from bwh ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Sunday, July 01, 2012 11:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

Can you give more info? Command line, description of data, where you got it from etc doug

On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Borzello, Mia

12:15 p.m.

i can fix this if I work with the identity matrix (emacs spm.reg.dat) after automatically coregistering (using spmregister), right?

thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, July 02, 2012 10:05 AM To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

Can you give more info? Command line, description of data, where you got it from etc doug

On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Borzello, Mia

1:23 p.m.

another question, i trying to pick points (electrode contacts) now, so at the command line i have: tkmedit BWXX_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz

but there is a strange bordering around the brain, and I'm unsure what to contribute it to or how to fix it. I've attached a screen shot of what's coming up.

thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, July 02, 2012 12:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

i can fix this if I work with the identity matrix (emacs spm.reg.dat) after automatically coregistering (using spmregister), right?

Can you give more info? Command line, description of data, where you got it from etc doug

On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Douglas N Greve

3 Jul 3 Jul

3:37 p.m.

Those are things that are in your ct.anat.mgz file. It's not a FreeSurfer problem. doug

On 07/02/2012 01:23 PM, Borzello, Mia wrote:

...

another question, i trying to pick points (electrode contacts) now, so at the command line i have: tkmedit BWXX_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz

but there is a strange bordering around the brain, and I'm unsure what to contribute it to or how to fix it. I've attached a screen shot of what's coming up.

thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, July 02, 2012 12:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

i can fix this if I work with the identity matrix (emacs spm.reg.dat) after automatically coregistering (using spmregister), right?

thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, July 02, 2012 10:05 AM To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

sure! at the command line: tkregister2 --s BWXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig this it's a CT of 124 slices from bwh ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Sunday, July 01, 2012 11:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

Can you give more info? Command line, description of data, where you got it from etc doug

On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Douglas N Greve

3:30 p.m.

I'm guessing that the registration failed (spmregister). If you want the identity, then you can just run tkregister2 with --regheader --reg reg.dat (It will create reg.dat when you hit the "save" button). But it will be unlikely that they will actually be in registration. doug

On 07/02/2012 12:15 PM, Borzello, Mia wrote:

...

i can fix this if I work with the identity matrix (emacs spm.reg.dat) after automatically coregistering (using spmregister), right?

thanks, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, July 02, 2012 10:05 AM To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

sure! at the command line: tkregister2 --s BWXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig this it's a CT of 124 slices from bwh ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Sunday, July 01, 2012 11:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] axial sheer

Can you give more info? Command line, description of data, where you got it from etc doug

On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help, Mia B.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Borzello, Mia
Borzello, Mia
Douglas Greve
Douglas N Greve