Dear all,
I am trying to prepare freesurfer surfaces for probtrackx fibertracking. I use the pial surfaces to stop fibers from going back into the white matter. In order to be able to track between hemispheres, the medial_wall labels have to be removed from these pial surfaces. I have difficulties finding out how to accomplish this. Is it possible to 'mask out' the medial wall label from the *h.pial surface, removing all the vertices and thus creating 'holes' in the surfaces?
Thank you very much,
Andries van der Leij
Hi Andries
you could use the cutting tools in tksurfer, although it sounds like this is something that we might want to make easier to do automatically.
cheers Bruce
On Mon, 25 Feb 2013, Andries R. Van Der Leij wrote:
Dear all,
I am trying to prepare freesurfer surfaces for probtrackx fibertracking. I use the pial surfaces to stop fibers from going back into the white matter. In order to be able to track between hemispheres, the medial_wall labels have to be removed from these pial surfaces. I have difficulties finding out how to accomplish this. Is it possible to 'mask out' the medial wall label from the *h.pial surface, removing all the vertices and thus creating 'holes' in the surfaces?
Thank you very much,
Andries van der Leij _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Ouch, I have quite some subjects. Luckily, with some help I found out you can reverse it, by using: annot2label with pial rm *Medial_wall* Label2surf (fsl) using a textfile containing all the other labels
This pretty much solves it.
Thank you again,
Andries
Sent from my iPhone
On Feb 25, 2013, at 21:37, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andries
you could use the cutting tools in tksurfer, although it sounds like this is something that we might want to make easier to do automatically.
cheers Bruce
On Mon, 25 Feb 2013, Andries R. Van Der Leij wrote:
Dear all,
I am trying to prepare freesurfer surfaces for probtrackx fibertracking. I use the pial surfaces to stop fibers from going back into the white matter. In order to be able to track between hemispheres, the medial_wall labels have to be removed from these pial surfaces. I have difficulties finding out how to accomplish this. Is it possible to 'mask out' the medial wall label from the *h.pial surface, removing all the vertices and thus creating 'holes' in the surfaces?
Thank you very much,
Andries van der Leij _______________________________________________ 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.
glad to hear it Bruce On Tue, 26 Feb 2013, Andries R. Van Der Leij wrote:
Hi Bruce,
Ouch, I have quite some subjects. Luckily, with some help I found out you can reverse it, by using: annot2label with pial rm *Medial_wall* Label2surf (fsl) using a textfile containing all the other labels
This pretty much solves it.
Thank you again,
Andries
Sent from my iPhone
On Feb 25, 2013, at 21:37, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Andries
you could use the cutting tools in tksurfer, although it sounds like this is something that we might want to make easier to do automatically.
cheers Bruce
On Mon, 25 Feb 2013, Andries R. Van Der Leij wrote:
Dear all,
I am trying to prepare freesurfer surfaces for probtrackx fibertracking. I use the pial surfaces to stop fibers from going back into the white matter. In order to be able to track between hemispheres, the medial_wall labels have to be removed from these pial surfaces. I have difficulties finding out how to accomplish this. Is it possible to 'mask out' the medial wall label from the *h.pial surface, removing all the vertices and thus creating 'holes' in the surfaces?
Thank you very much,
Andries van der Leij _______________________________________________ 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@nmr.mgh.harvard.edu
-
Andries R. Van Der Leij -
Bruce Fischl