no definitely not "w" format, which we don't use for anything anymore.
YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham
wrote:
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It would appear not, as I'm getting an error on my pial output files but not
my white ones. Here are my commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial --trgsubject
fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial --trgsubject
fs_target --trgsurfval ./registered_rh.pial --trg_type w
The white calls output seems to be fine, but the pial ones aren't. I
somewhat naively trued trg_type pial but that wasn't correct.
On 05/05/2020 17:33, Ian Hardingham wrote:
Thanks Bruce, extremely helpful.
Can I just check that the "w" format is what is used by both the
lh/rh.pial and the lh/rh.white files? I only ask because my
surf2surf command outputs the exact output filename if the end
is ".white", but if it's ".pial" it outputs ".pial.w", which I
find a little curious.
Ian
On 05/05/2020 16:34, Bruce Fischl wrote:
yes, check out options like:
--sval-xyz
if you need further help though I'll have to defer to Doug
:)
Bruce
On Tue, 5 May 2020, Ian Hardingham wrote:
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Bruce, I've read the docs on mri_surf2surf - I
wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and
rh.white) rather than values for
something such as thickness - is there an
option for mri_surf2surf to allow
this?
On 05/05/2020 14:43, Bruce Fischl wrote:
Hi Ian
you can use mri_surf2surf to map
surfaces between subjects, but
our atlas isn't really a surface. You
can use the surfaces in
the fsaverage dir, but they are meant
for visualization and are
much smoother than individuals
cheers
Bruce
On Tue, 5 May 2020, Ian wrote:
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Caution
Hi Freesurfers.
I have a subject S with recon-all
having been run on
it.
I have the subject-specific
surface files
/surf/lh.pial, rh.pial, lh.white,
and rh.white.
I would like an Atlas's lh.pial,
rh.pial, lh.white,
and rh.white in subject
space.
Any helpers on how to achieve
this?
Thanks,
Ian
--
Ian Hardingham
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