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
wrote:
you should be able to load it into tksurfer as an ov
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
wrote:
> you should be able to load it into tksurfer as an overlay.
>
> cheers
> Bruce
>
> On Mon, 13 May 2013, Jonathan DuBois wrote:
>
> Hi B
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 anythi
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
It cannot create a label file directly. What happens when you try to
load it as an overlay? Make sure to set the threshold to 0.5. Also,
before going to the surface load the binary volume onto the anatomical
with the surfaces to make sure that the surfaces pass through the mask.
doug
On 5/1
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 --m
I used the following options: mri_vol2surf --hemi lh --regheader subject01
--cortex --mov label.mgz --o ./label.mgh
It 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 fi
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 J
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
> freevi
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
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
the
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 regis
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.
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