Dear FS list,
We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1).
I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere?
Thank you, Tanja.
Hi Tanja,
Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
But if part of the brain is missing only after you added control points and ran -autorecon2-cp -autorecon3, then please check if any of the control points were placed in GM or really close to GM.
Sita.
On Wed, 7 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1).
I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere?
Thank you, Tanja.
Thank you, Sita, for your reply.
1. The skull strip was good, the cortex disappeared after we added cp. I removed control points and put new ones that are surely in wm, now re-running.
2. I have one more question: I did previous analysis with FS5.0 on 1.5T data with non-isotropic voxels. Now for FS5.1 we use 3T images with 1x1x1mm voxels. For previous analysis the error, when a part of occipital cortex is excluded, appeared in around 1 per 40 cases. Now with better data and newer version we have this problem in around 1 per 5 cases. The only idea I can think of is increased inhomogeniety in field due to increased static field of scanner. Can it be true? Can you suggest other possible reasons?
Thank you, Tanja.
On Wed, Mar 7, 2012 at 4:29 PM, Sita Kakunoori sita@nmr.mgh.harvard.edu wrote:
Hi Tanja,
Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
But if part of the brain is missing only after you added control points and ran -autorecon2-cp -autorecon3, then please check if any of the control points were placed in GM or really close to GM.
Sita.
On Wed, 7 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1).
I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere?
Thank you, Tanja.
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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.
Hi Tanja,
yes, 3T will have more dielectric/RF penetration inhomogeneity than 1.5T. There was also a change to recon-all that caused the control points to be applied to the subcortical normalize as well as cortical (previously it was just cortical) that a number of people have now reported messes things up, so we are going to back it out. We will distribute a new recon-all that reverts to the previous behavior sometime soon (right Nick?).
sorry for the problems. Bruce
On Thu, 8 Mar 2012, Tetiana Dadakova wrote:
Thank you, Sita, for your reply.
- The skull strip was good, the cortex disappeared after we added cp.
I removed control points and put new ones that are surely in wm, now re-running.
- I have one more question: I did previous analysis with FS5.0 on
1.5T data with non-isotropic voxels. Now for FS5.1 we use 3T images with 1x1x1mm voxels. For previous analysis the error, when a part of occipital cortex is excluded, appeared in around 1 per 40 cases. Now with better data and newer version we have this problem in around 1 per 5 cases. The only idea I can think of is increased inhomogeniety in field due to increased static field of scanner. Can it be true? Can you suggest other possible reasons?
Thank you, Tanja.
On Wed, Mar 7, 2012 at 4:29 PM, Sita Kakunoori sita@nmr.mgh.harvard.edu wrote:
Hi Tanja,
Sorry if I missed something but was the cortex stripped off even before you made any edits. If so, it's probably skull strip error. Please refer to this wiki for instructions to correct the error.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
But if part of the brain is missing only after you added control points and ran -autorecon2-cp -autorecon3, then please check if any of the control points were placed in GM or really close to GM.
Sita.
On Wed, 7 Mar 2012, Tetiana Dadakova wrote:
Dear FS list,
We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1).
I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere?
Thank you, Tanja.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Sita Kakunoori -
Tetiana Dadakova