the orig.mgz is also changed to 1 byte/voxel. The norm.mgz is in the same
space, but with the skull removed and the subcortical intensity
normalization run on it. All the volumes in fact in the mri dir except
rawavg.mgz are in the same coords
cheers
Bruce
On Mon, 25 Mar 2013, Joshua Lee wrote:
I see. To clarify. orig is the conformed version of the original input file,
which means just sampling to 1 mm as needed, and cropping to 256 matrix.
norm.mgz has some intensity corrections, but does not include spatial
changes.
I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
and I thought that maybe that spatial warping was involved beyond resampling
to the original dimensions/resolution to get to "native space". This
simplifies things greatly. Thank you both.
On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Josh,
there are no spatial transforms to go from orig to norm. They
are in the same space.
cheers
Bruce
On Mon, 25 Mar 2013, Joshua Lee wrote:
Hi Doug,
Is a standard 12 affine registration sufficient to
get a subjects structural
(in a different orientation) into the same space as
norm.mgz, or will I need
some non-linear registration? Basically, what kind
of transforms are applied
to go from orig to norm?
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee
<jki...@ucdavis.edu> wrote:
Hi Doug.
That was in fact what I decided to do.
Thanks!
Josh
-
J
On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu> wrote:
Can you compute the registration between the
manually
traced anat space
and the FS conformed space? Eg, with BBR. If
you can do
that, then you
can run mri_label2vol to convert the mask into
FS
conformed space
(assuming that that is what you want to do).
doug
On 03/22/2013 04:43 PM, Joshua Lee wrote:
> Hi All,
>
> I wanted to get peoples advice on the best
method of
> registration/interpolation to use on a
manually traced
segmentation
> (and its structural) that is not in the same
space and
orientation as
> the structurals I started Freesurfer with
(although they
both
> originally came from the same image. I want
to maintain
the integrity
> of the manual traced binary mask through
this
registration and
> reslice. For a number of reasons, I do not
want to take
Freesurfers
> output to the space of the manual
segmentation.
>
> What do people think is a good technique?
Flirt nearest
neighbor
> interpolation? Something different from
Freesurfer?
ANTs?
> -
> Josh
>
>
> _______________________________________________
> 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
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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.
