no worries. I hope it works for you
Bruce
On Fri, 24 Apr 2015, Kirstie Whitaker
wrote:
Thank you - right as you sent your reply I was writing an apology because
I'd just seen that flag.
It's Friday evening here in the UK and it might be time to stop sending
emails for a little while!
So sorry! And thank you!
Kx
On 24 April 2015 at 18:33, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Kirstie
you can pick the interpolation method with
--interp <string>
where string is one of:
nearest
trilinear
sinc
cubic
cheers
Bruce
On Fri, 24 Apr 2015, Kirstie Whitaker wrote:
I'm sorry, I did wonder if my email wasn't clear as
soon as I clicked send.
I'm using mri_vol2surf and I've read the --help
output and this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf
The help is very clear about which surface the
volume is being sampled to
etc, but I can't see a section that describes
exactly how the values are
interpolated (if they're interploated) onto the
surface.
The assumption that I was trying to clarify in my
(too short) email was that
the voxel through which the vertex passes is the
value that is mapped to
that vertex.
Possible alternatives would be some sort of weighted
sum of the neighboring
voxels, perhaps, but I had assumed that if there
were interpolations
happening it would be mentioned in the help file?
Does this make sense? I do apologise if I've missed
an obvious reference
that explains all this!
Best wishes
Kx
On 24 April 2015 at 17:38, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Kirstie
I think you get to decide how you want the
sampling done in
mri_vol2surf.
cheers
Bruce
On Fri, 24 Apr 2015, Kirstie Whitaker wrote:
Thank you Bruce - that's excellent and
works
perfectly.
Can I ask - when I sample from the new
surface from
a volume is it the voxel
value in which the vertex lands that is
assigned to
the vertex or is there
any interpolation across multiple voxels
before
assigning the vertex a
value?
Thanks again for the help!
Kx
On 20 April 2015 at 14:46, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Kirstie
you can do this with mris_expand.
For example:
mris_expand -thickness lh.white
0.5 lh.graymid
will generate a surface halfway
between white
and pial. Using
that surface
to sample is probably a better
method than
using profrac,
although I expect
the differences will be small
unless you have
very highres
data.
cheers
Bruce
On Mon, 20 Apr 2015, Kirstie
Whitaker wrote:
> Hi experts,
>
> I've used the command
mri_vol2surf with the
--projfrac 0.5
flag to sample a
> volume halfway between the pial
and white
matter surfaces.
>
> I was wondering if there was a
way to
visualise where this
surface lay on
> the volume? Ideally I'd like to
show a
figure with the pial,
white and this
> halfway surface overlayed on the
volume.
>
> Any ideas?
>
> Thank you
> Kirstie
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> Mailing Address
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> Phone: +44 7583 535 307
> Website: www.kirstiewhitaker.com
>
>
_______________________________________________
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.
--
Kirstie Whitaker, PhD
Research Associate
Department of Psychiatry
University of Cambridge
Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB
Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
_______________________________________________
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.
--
Kirstie Whitaker, PhD
Research Associate
Department of Psychiatry
University of Cambridge
Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB
Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
_______________________________________________
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.
--
Kirstie Whitaker, PhD
Research Associate
Department of Psychiatry
University of Cambridge
Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB
Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
_______________________________________________
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.
