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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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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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