Hi Michael,
yes, you can do this in tksurfer with a tcl script (labl_erode and
labl_dilate I believe). Not sure if there is a binary to do it, but it
would be pretty easy to write
Bruce
On Mon, 16 Jul 2012, Michael Waskom wrote:
Hmm, ok. Are there no functions for doing a dilation/erosion on a surface
label?
On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
There is not an easy/good way to handle this situation. The way
it works
is that it goes through each point in the source and finds the
closest
vertex in the target. If the target is more densely sampled,
then there
are some points in the target in the middle of the label that
are not
the closest vertex to any label vertex in the source. It is hard
to
figure out computationally whether an unlabeled point is in the
middle
of the label or halfway around the brain. One thing that might
work ok
is to save the output as a binary mask (--outmask), then smooth
it a
little (mris_fwhm or mri_surf2surf), then re-binarize the mask
(mri_binarize), then convert it to a label (mri_cor2label --i
smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white
--o
lh.label.yoursubject).
doug
On 07/16/2012 03:30 PM, Michael Waskom wrote:
> Hi, just wanted to bump this up since it looks like Doug is
back.
>
> On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom
<mwas...@stanford.edu
> <mailto:mwas...@stanford.edu>> wrote:
>
> Hi,
>
> I'm using mri_label2label to reverse normalize labels from
fsaverage
> space to the native surface.
>
> I'm ending up with some splotchy-looking labels, for lack of a
better
> word. See what I mean here:
> http://web.mit.edu/mwaskom/www/splotchy.png
>
> I'm doing this normalization in a script with the following
relevant
> line, which seems to be what happens inthe BAlabes step of
recon-all
>
> mri_label2label --srclabel
../fsaverage/label/${hemi}.${roi}.label \
> --srcsubject fsaverage --trgsubject ${subj} \
> --trglabel label/$hemi.${roi}.label \
> --regmethod surface --hemi $hemi
>
> Any idea how I can avoid this splotchiness or, failing that, do
a
> closing on the label to clean up some of the noise?
>
> Cheers,
> Michael
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________
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
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.
