Dear Bruce/freesurfer community,
Thank-you for offering to take a look at our data.
I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and Subject_After_Cpedit.zip. Please let me know if you haven't received them. I uploaded these last Friday but haven't as yet had a reply.
I did this as a test as I assumed that a single ctrl point in WM would have no effect on the surfaces. The 1 ctrl point was added to the LH WM in temporal cortex (slice 120).
Thank-you for your help, it would be great if we could find a solution to this problem.
- Vanessa
On 12/10/12 1:24 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Vanessa
if you can upload an example (the entire subject dir) before adding the single control point you refer to, and after adding it we'll track it down.
thanks Bruce
On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote:
Hi all,
I have seen others post a similar problem on the freesurfer mailing list but I could not find a solution.
When I edit a volume using control points, I am noticing that the use of CP edits adversely effects the wm/gm surfaces in the resulting re-processed image. Like others have reported, the surfaces are adversely affected in locations distant from the CP edits. The temporal lobes are particularly affected.
We are using freesurfer 5.1. I have noticed the following things:
- The problem occurs irrespective of the number of control points added, i.e. whether >100 or <10 control points added
- The problem occurred when only one CP was added in a voxel that was clearly wm
- The problem did not occur after reprocessing with FS 4.5
- I have tried the flag to disable mri_ca_normalize when reprocessing with ?autorecon2. This did not seem to help. I used the command: recon-all ?nocanorm ?autorecon2-cp ?subjid $SUBJ
I have screenshots available that illustrate the changes in the surfaces after reprocessing.
Could anyone help with this problem?
Thank-you,
Vanessa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
------ End of Forwarded Message
Hi Vanessa I'm running some tests now Bruce
On Oct 15, 2012, at 9:10 PM, Vanessa Louise Cropley vcropley@unimelb.edu.au wrote:
Dear Bruce/freesurfer community,
Thank-you for offering to take a look at our data.
I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and Subject_After_Cpedit.zip. Please let me know if you haven't received them. I uploaded these last Friday but haven't as yet had a reply.
I did this as a test as I assumed that a single ctrl point in WM would have no effect on the surfaces. The 1 ctrl point was added to the LH WM in temporal cortex (slice 120).
Thank-you for your help, it would be great if we could find a solution to this problem.
- Vanessa
On 12/10/12 1:24 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Vanessa
if you can upload an example (the entire subject dir) before adding the single control point you refer to, and after adding it we'll track it down.
thanks Bruce
On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote:
Hi all,
I have seen others post a similar problem on the freesurfer mailing list but I could not find a solution.
When I edit a volume using control points, I am noticing that the use of CP edits adversely effects the wm/gm surfaces in the resulting re-processed image. Like others have reported, the surfaces are adversely affected in locations distant from the CP edits. The temporal lobes are particularly affected.
We are using freesurfer 5.1. I have noticed the following things:
- The problem occurs irrespective of the number of control points added, i.e. whether >100 or <10 control points added
- The problem occurred when only one CP was added in a voxel that was clearly wm
- The problem did not occur after reprocessing with FS 4.5
- I have tried the flag to disable mri_ca_normalize when reprocessing with ?autorecon2. This did not seem to help. I used the command: recon-all ?nocanorm ?autorecon2-cp ?subjid $SUBJ
I have screenshots available that illustrate the changes in the surfaces after reprocessing.
Could anyone help with this problem?
Thank-you,
Vanessa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
------ End of Forwarded Message
Thank-you Bruce!
On 16/10/12 12:25 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Vanessa I'm running some tests now Bruce
On Oct 15, 2012, at 9:10 PM, Vanessa Louise Cropley vcropley@unimelb.edu.au wrote:
Dear Bruce/freesurfer community,
Thank-you for offering to take a look at our data.
I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and Subject_After_Cpedit.zip. Please let me know if you haven't received them. I uploaded these last Friday but haven't as yet had a reply.
I did this as a test as I assumed that a single ctrl point in WM would have no effect on the surfaces. The 1 ctrl point was added to the LH WM in temporal cortex (slice 120).
Thank-you for your help, it would be great if we could find a solution to this problem.
- Vanessa
On 12/10/12 1:24 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Vanessa
if you can upload an example (the entire subject dir) before adding the single control point you refer to, and after adding it we'll track it down.
thanks Bruce
On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote:
Hi all,
I have seen others post a similar problem on the freesurfer mailing list but I could not find a solution.
When I edit a volume using control points, I am noticing that the use of CP edits adversely effects the wm/gm surfaces in the resulting re-processed image. Like others have reported, the surfaces are adversely affected in locations distant from the CP edits. The temporal lobes are particularly affected.
We are using freesurfer 5.1. I have noticed the following things:
- The problem occurs irrespective of the number of control points added, i.e. whether >100 or <10 control points added
- The problem occurred when only one CP was added in a voxel that was clearly wm
- The problem did not occur after reprocessing with FS 4.5
- I have tried the flag to disable mri_ca_normalize when reprocessing with ?autorecon2. This did not seem to help. I used the command: recon-all ?nocanorm ?autorecon2-cp ?subjid $SUBJ
I have screenshots available that illustrate the changes in the surfaces after reprocessing.
Could anyone help with this problem?
Thank-you,
Vanessa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
------ End of Forwarded Message
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Vanessa Louise Cropley