sure, glad it's working
Bruce
On Mon, 13 May 2013, Jonathan DuBois wrote:
Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks for
your help!
Best,
Jonathan
On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
you should be able to load it into tksurfer as an overlay.
cheers
Bruce
On Mon, 13 May 2013, Jonathan DuBois wrote:
Hi Bruce,
Thanks for your help yesterday. I was able to create the .mgh file
using the -output_type mgh option,
but I am still unable to
load it in tksurfer as label or anything else. If you or Doug have
any other suggestions, I would really
appreciate it. Thanks!
Jonathan
On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Jonathan
try -output_type mgh. It should create a "volume" that is
nvertices long. Not sure if it can
directly create a label
file, maybe Doug knows?
Bruce
On Sun, 12 May 2013, Jonathan DuBois wrote:
I used the following options: mri_vol2surf --hemi lh
--regheader subject01
--cortex --mov label.mgz --o ./label.mghIt ran without error, but I
could
not open the resulting file in tksurfer as either a label or an
overlay:
---------
/Applications/freesurfer/tktools/tksurfer.bin: no data in label file
/Users/label.mgh
tkmedit: Trying to open /Users/label.dat
surfer: Interpreting overlay volume /Users/label.mgh as encoded
scalar
volume
Best,
Jonathan
On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
try using --regheader
cheers
Bruce
On Sun, 12 May 2013, Jonathan DuBois wrote:
Hi Bruce,
I would like to convert the .mgz label volume to a
surface label for that
subject, but mri_vol2surf requires a registration
file.
Best,
Jonathan
On Sunday, May 12, 2013, Bruce Fischl wrote:
Hi Jonathan
you don't need to register it if it's shown
properly in tkmedit
or freeview. Can you tell us more about what
you are trying to
do?
Bruce
On Sun, 12 May 2013, Jonathan DuBois wrote:
Hi Bruce,
Thanks for the quick response. The label
is a
manually traced area of the
cortex. It is in subject scanner space
and has a
single value, so it
probably would not work with bbregister.
I can load
it in tkmedit as a
segmentation and the alignment is
correct. I
attached a screenshot. Is there
a way to select the values greater than
zero in
tkmedit and save as a label
that could be used in vol2surf? I have
other labels
that are larger so I
would prefer not to retrace them if
possible.
Inline image 2
Best,
Jonathan
On Sun, May 12, 2013 at 10:11 AM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Jonathan
what is the label? What space is
it in? If it
has gray/white
contrast you could try bbregister.
cheers
Bruce
On Sat, 11 May 2013, Jonathan
DuBois wrote:
Hi Freesurfer Experts,
I have a binary volume label
in subject
space that I
converted from MINC to MGZ.
I would like
to register
it to
the surface of that subject
as a flat
label. I
thought I would be able to
do so with
mri_vol2surf
but I am not
sure how to generate the
required
registration file.
Is that the correct command,
and if so,
which
registration
file should I use?
Thanks
Jonathan
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.
