Hi,

This (recon-all after wm.mgz and brainmask.mgz edits) didn't work. The part that wasn't included in the pial or white matter surfaces is still not included. The intensities in the white matter regions are no different than in white matter regions that were included in the white matter. Any other suggestions?

Thanks, Allie

On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen rosen.allie@gmail.com wrote:

Hi Bruce,

I am running recon-all tonight using wm voxels that I manually added (I also edited brainmask.mgz to add missing grey matter). To me it doesn't really look like a case of the white matter not having a high enough intensity. It simply looks like the whole lobe was ignored, regardless of intensity. But I'll check tomorrow to see if the intensity is low.

Thanks, Allie

On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

What is the intensity of the white matter in the regions you drew in? A couple of control points might help if it is less than 110

On Apr 18, 2011, at 12:36 PM, Allie Rosen rosen.allie@gmail.com wrote:

Hi Sita,

Thanks for all the responses! I've actually had the same problem for multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum as well. I've attached pictures of where I am adding wm voxels. They aren't really in the same places as in the online tutorials. Could you take a quick look to see if they're in the right place?

Thanks, Allie

On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori <sita@nmr.mgh.harvard.edu sita@nmr.mgh.harvard.edu> wrote:

...

Hi Allie,

pial surface which looks like this can only be corrected by correcting the wm.mgz. Also I would suggest to try and fix the cerebellum and see if it corrects the surfaces as well. Since part of the cerebellum is stripped off, it's probably affecting the segmentation as well but I could be wrong. what version of freesurfer are you using.

Sita.

On Mon, 18 Apr 2011, Allie Rosen wrote:

Hi Sita,

...

Can I still add voxels to wm.mgz even though the points would be outside even the pial boundary?

Thanks Allie

On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori < sita@nmr.mgh.harvard.edusita@nmr.mgh.harvard.edu>wrote:

...

Hi Allie,

This probably needs white matter edits but it's hard to tell from one slice. Please refer to our white matter edits wiki and toplogical defects wiki and see if it helps in fixing the errors in your datasets. Also it looks like part of the Cerebellum is stripped off. You might want to correct that as well.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect

Sita.

On Mon, 18 Apr 2011, Allie Rosen wrote:

Hi,

...

Once processed, several of my subjects have had errors around the occipital lobe. Attached is an example. I've already tried editing brainmask.mgz and running recon-all, but as you can see, this didn't change the pial or wm borders. What can I do to fix this?

Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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 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.

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Upload the subject and we will take a look

On Apr 19, 2011, at 8:03 AM, Allie Rosen rosen.allie@gmail.com wrote:

Hi,

This (recon-all after wm.mgz and brainmask.mgz edits) didn't work. The part that wasn't included in the pial or white matter surfaces is still not included. The intensities in the white matter regions are no different than in white matter regions that were included in the white matter. Any other suggestions?

Thanks, Allie

On Mon, Apr 18, 2011 at 7:53 PM, Allie Rosen rosen.allie@gmail.com wrote: Hi Bruce,

I am running recon-all tonight using wm voxels that I manually added (I also edited brainmask.mgz to add missing grey matter). To me it doesn't really look like a case of the white matter not having a high enough intensity. It simply looks like the whole lobe was ignored, regardless of intensity. But I'll check tomorrow to see if the intensity is low.

Thanks, Allie

On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: What is the intensity of the white matter in the regions you drew in? A couple of control points might help if it is less than 110

On Apr 18, 2011, at 12:36 PM, Allie Rosen rosen.allie@gmail.com wrote:

...

Hi Sita,

Thanks for all the responses! I've actually had the same problem for multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum as well. I've attached pictures of where I am adding wm voxels. They aren't really in the same places as in the online tutorials. Could you take a quick look to see if they're in the right place?

Thanks, Allie

On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori sita@nmr.mgh.harvard.edu wrote:

Hi Allie,

pial surface which looks like this can only be corrected by correcting the wm.mgz. Also I would suggest to try and fix the cerebellum and see if it corrects the surfaces as well. Since part of the cerebellum is stripped off, it's probably affecting the segmentation as well but I could be wrong. what version of freesurfer are you using.

Sita.

On Mon, 18 Apr 2011, Allie Rosen wrote:

Hi Sita,

Can I still add voxels to wm.mgz even though the points would be outside even the pial boundary?

Thanks Allie

On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori sita@nmr.mgh.harvard.eduwrote:

Hi Allie,

This probably needs white matter edits but it's hard to tell from one slice. Please refer to our white matter edits wiki and toplogical defects wiki and see if it helps in fixing the errors in your datasets. Also it looks like part of the Cerebellum is stripped off. You might want to correct that as well.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect

Sita.

On Mon, 18 Apr 2011, Allie Rosen wrote:

Hi,

Once processed, several of my subjects have had errors around the occipital lobe. Attached is an example. I've already tried editing brainmask.mgz and running recon-all, but as you can see, this didn't change the pial or wm borders. What can I do to fix this?

Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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.

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