Hi all,
We have a series of labels (over 100) that encompass the majority of the cortex, but some minute vertices remained unlabeled. We've tried several attempts to make this .annot file and as well as attempts to label the unlabeled vertices (from a previous post 'labeling unlabeled vertices..'). But still to no avail.
Question: how to convert .label files to .annot file, when some vertices are still unassigned.
Thanks!!!
Hi Sam
from the tksurfer tcl interface you can call
% read_and_smooth_parcellation <parc name> <lut name> <siter> <miter>
where siter is the number of soap bubble smoothing iterations that will fill in the holes, and miter are the # of mode filter iterations that will smooth out rough edges.
cheers Bruce
On Wed, 30 May 2012, Sam Carpenter wrote:
Hi all,
We have a series of labels (over 100) that encompass the majority of the cortex, but some minute vertices remained unlabeled. We've tried several attempts to make this .annot file and as well as attempts to label the unlabeled vertices (from a previous post 'labeling unlabeled vertices..'). But still to no avail.
Question: how to convert .label files to .annot file, when some vertices are still unassigned.
Thanks!!!
Hi,
To clarify, we don¹t have a complete parcellation scheme. It looks like that command requires an .annot file. If I'm not mistaken, this script does not appear to assign them all to a label but to other existing labels.
We have a collection of .label files that have we are unable to convert to a .annot file >>> it appears that it does not work because not all of the vertices are assigned by our labels. We're looking for a straightforward solution to assigning these unlabeled vertices to their own label.
- Thanks so much for the quick reply though Bruce!
On 5/30/12 2:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Sam
from the tksurfer tcl interface you can call
% read_and_smooth_parcellation <parc name> <lut name> <siter> <miter>
where siter is the number of soap bubble smoothing iterations that will fill in the holes, and miter are the # of mode filter iterations that will smooth out rough edges.
cheers Bruce
On Wed, 30 May 2012, Sam Carpenter wrote:
Hi all,
We have a series of labels (over 100) that encompass the majority of the cortex, but some minute vertices remained unlabeled. We've tried several attempts to make this .annot file and as well as attempts to label the unlabeled vertices (from a previous post 'labeling unlabeled vertices..'). But still to no avail.
Question: how to convert .label files to .annot file, when some vertices are still unassigned.
Thanks!!!
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 Sam
I guess I don't understand what you want. You have some vertices that are not labeled because you don't want them to be, but others that are not labeled but you do want them to be?
Bruce On Wed, 30 May 2012, Sam Carpenter wrote:
Hi,
To clarify, we don¹t have a complete parcellation scheme. It looks like that command requires an .annot file. If I'm not mistaken, this script does not appear to assign them all to a label but to other existing labels.
We have a collection of .label files that have we are unable to convert to a .annot file >>> it appears that it does not work because not all of the vertices are assigned by our labels. We're looking for a straightforward solution to assigning these unlabeled vertices to their own label.
- Thanks so much for the quick reply though Bruce!
On 5/30/12 2:33 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Sam
from the tksurfer tcl interface you can call
% read_and_smooth_parcellation <parc name> <lut name> <siter> <miter>
where siter is the number of soap bubble smoothing iterations that will fill in the holes, and miter are the # of mode filter iterations that will smooth out rough edges.
cheers Bruce
On Wed, 30 May 2012, Sam Carpenter wrote:
Hi all,
We have a series of labels (over 100) that encompass the majority of the cortex, but some minute vertices remained unlabeled. We've tried several attempts to make this .annot file and as well as attempts to label the unlabeled vertices (from a previous post 'labeling unlabeled vertices..'). But still to no avail.
Question: how to convert .label files to .annot file, when some vertices are still unassigned.
Thanks!!!
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
-
Bruce Fischl -
Sam Carpenter