The internal representation of the label format is treated differently
between tkmedit and tksurfer. Labels are lists of RAS coords. When you
load one into tkmedit, it converts each RAS coord to a voxel index for
its internal data structure. When you save it out, it converts the voxel
index to an RAS coord, but this can be different than the original RAS
coord because it is always the corner of the voxel, where as the original
point can be anywhere inside the voxel. However, when tksurfer loads the
label, even though the RAS coords in the label don't match exactly with
the RAS coords of the surface vertices, it should find the closest vertex
coord for each RAS coord, and add that to the label.
Can you send the output that tksurfer makes to the shell when you load a
label that becomes fragmented like this?
On Thu, 11 Aug 2005, Fornito, Alexander wrote:
Hi Kevin,
It shouldn't.
I created the labels by the doing the following:
1 - manully raced an ROI using another program (Analyze) in volume space and
saved the ROI as a greyscale mask in analyze format
2 - used mri_convert to convert both the original T1 and ROI to COR format.
3 - Generated the surface of the T1 and loaded the ROI as an overlay in tksurfer
4 - Filled the overlay using custom fill and saved it as a label.
I'm not sure how I would check the image dimensions of the label, but I assume
step 2 would have put it into 1mm3, which would then convert to 1mm2 when
projected onto the surface (?).
-----Original Message-----
From: Kevin Teich [mailto:[EMAIL PROTECTED]
Sent: Thu 8/11/2005 5:18 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Editing labels
I've been trying to edit some labels in tkmedit and have noticed that if
I save a label in tkmedit and then project it back onto the surface in
tksurfer, it appears fragmented (ie., speckled). This happens even if I
save a label that was created in tksurfer in tkmedit without even
editing it (ie., create label in tksurfer, load it in tkmedit, save it
in tkmedit (without editing), and then load it back in tksurfer). I
don't understand why this should happen, particulalry in the latter
case, as the label should remain unchanged. Can anyone explain why this
might happen? Thanks, Alex
Does your data have a voxel resolution different than 1mm squared?
--
Kevin Teich
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
