Would it be a problem to skip this step by using the -notal-check or would that mess the results up too much?
On 10/6/09 2:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That might be a problem as (I think) our target is made from 3T data, and the contrast might be different. Pratap, is your anatomical data from 1.5T?
Weisinger, Brian (NIH/OD) [E] wrote:
These images are from a 1.5 scanner
On 10/6/09 12:24 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It means that you don't have permission to write into that directory.
The images look a little off. What kind of scanner are you using?
doug
Weisinger, Brian (NIH/OD) [E] wrote:
When I try to use tkregister2 I get this message, how do I go about changing not being able to save the changes I make.
WARNING: cannot write to /Applications/freesurfer/subjects/00007/mri/transforms. You will not be able to save any edits. Hit Enter to continue:
Also I just wanted to get your opinion about these images...It looks like I need to stretch them some so that the green part is in the white brain area. Would you agree?
[cid:3337666238_142370727]
[cid:3337666238_142392223]
[cid:3337666238_142372460]
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Depends on what you want to do with it. It probably won't affect the surface/subcortical analysis. But if you try to report tal coordinates for this subject or try to make an average subject using this subject (and/or other subjects that have a bad tal), then the coordinates will be off.
doug
Weisinger, Brian (NIH/OD) [E] wrote:
Would it be a problem to skip this step by using the -notal-check or would that mess the results up too much?
On 10/6/09 2:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That might be a problem as (I think) our target is made from 3T data, and the contrast might be different. Pratap, is your anatomical data from 1.5T?
Weisinger, Brian (NIH/OD) [E] wrote:
These images are from a 1.5 scanner
On 10/6/09 12:24 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It means that you don't have permission to write into that directory.
The images look a little off. What kind of scanner are you using?
doug
Weisinger, Brian (NIH/OD) [E] wrote:
When I try to use tkregister2 I get this message, how do I go about changing not being able to save the changes I make.
WARNING: cannot write to /Applications/freesurfer/subjects/00007/mri/transforms. You will not be able to save any edits. Hit Enter to continue:
Also I just wanted to get your opinion about these images...It looks like I need to stretch them some so that the green part is in the white brain area. Would you agree?
[cid:3337666238_142370727]
[cid:3337666238_142392223]
[cid:3337666238_142372460]
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
So if I wanted to do the longitudinal stream it would be important to fix these then. Is it possible to do this longitudinal stream if the scanner was a 1.5t and therefore the talairach will be off since the target was 3t and the contrast may be off?
On 10/6/09 2:23 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Depends on what you want to do with it. It probably won't affect the surface/subcortical analysis. But if you try to report tal coordinates for this subject or try to make an average subject using this subject (and/or other subjects that have a bad tal), then the coordinates will be off.
doug
Weisinger, Brian (NIH/OD) [E] wrote:
Would it be a problem to skip this step by using the -notal-check or would that mess the results up too much?
On 10/6/09 2:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That might be a problem as (I think) our target is made from 3T data, and the contrast might be different. Pratap, is your anatomical data from 1.5T?
Weisinger, Brian (NIH/OD) [E] wrote:
These images are from a 1.5 scanner
On 10/6/09 12:24 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It means that you don't have permission to write into that directory.
The images look a little off. What kind of scanner are you using?
doug
Weisinger, Brian (NIH/OD) [E] wrote:
When I try to use tkregister2 I get this message, how do I go about changing not being able to save the changes I make.
WARNING: cannot write to /Applications/freesurfer/subjects/00007/mri/transforms. You will not be able to save any edits. Hit Enter to continue:
Also I just wanted to get your opinion about these images...It looks like I need to stretch them some so that the green part is in the white brain area. Would you agree?
[cid:3337666238_142370727]
[cid:3337666238_142392223]
[cid:3337666238_142372460]
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I don't think it will affect the longitudinal stream, but Martin would know more.
Weisinger, Brian (NIH/OD) [E] wrote:
So if I wanted to do the longitudinal stream it would be important to fix these then. Is it possible to do this longitudinal stream if the scanner was a 1.5t and therefore the talairach will be off since the target was 3t and the contrast may be off?
On 10/6/09 2:23 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Depends on what you want to do with it. It probably won't affect the surface/subcortical analysis. But if you try to report tal coordinates for this subject or try to make an average subject using this subject (and/or other subjects that have a bad tal), then the coordinates will be off.
doug
Weisinger, Brian (NIH/OD) [E] wrote:
Would it be a problem to skip this step by using the -notal-check or would that mess the results up too much?
On 10/6/09 2:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That might be a problem as (I think) our target is made from 3T data, and the contrast might be different. Pratap, is your anatomical data from 1.5T?
Weisinger, Brian (NIH/OD) [E] wrote:
These images are from a 1.5 scanner
On 10/6/09 12:24 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It means that you don't have permission to write into that directory.
The images look a little off. What kind of scanner are you using?
doug
Weisinger, Brian (NIH/OD) [E] wrote:
When I try to use tkregister2 I get this message, how do I go about changing not being able to save the changes I make.
WARNING: cannot write to /Applications/freesurfer/subjects/00007/mri/transforms. You will not be able to save any edits. Hit Enter to continue:
Also I just wanted to get your opinion about these images...It looks like I need to stretch them some so that the green part is in the white brain area. Would you agree?
[cid:3337666238_142370727]
[cid:3337666238_142392223]
[cid:3337666238_142372460]
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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Weisinger, Brian (NIH/OD) [E]