I would also question what you hope to accomplish by using the native
freesurfer mesh - the fMRI data doesn't have that kind of resolution, and
the result of resampling to it means you can't compare across subjects
without resampling again later. Surface resampling is also unlike volume
resampling, in that it doesn't move any of the subjects data in anatomical
space (the T1w folder contains surfaces with acpc rigid aligned anatomical
locations - you probably just want to use the 32k midthicknesses from
there, as opposed to the ones in MNINonLinear) - think of it as changing
the sampling "grid" (mesh), not as a spatial warp. The trick of surface
registration is that we can give the same mesh of samples different
coordinates per-subject - we use the index in the mesh for the purpose of
matching functional identity as best as we can, but the coordinates remain
wherever that point was in the individual's anatomy. Even the coordinates
of the individual MNINonLinear surfaces are different, both because the
volume alignment doesn't fully match gray matter across subjects, and from
when our estimate of functional location disagrees with a folding-based
alignment (since aligning T1w images basically tries to align folding).
FYI, the error message you are getting is because you specified the 164k
spheres, while the 91282 grayordinate cifti data exists on the 32k mesh (so
you would need to use the 32k spheres).
Tim
On Fri, Sep 28, 2018 at 8:20 PM, Jacob Miller <jacob_mil...@berkeley.edu>
wrote:
> Hi all,
>
> I am interested in performing a resting state analysis in native surface
> space, using the surface cifti *.dtseries files. I am trying to resample
> these files to an individual subject's native surface space using
> -cifti-resample, but am running into trouble. When I run the following code:
>
> *L_template='standard.L.sphere.164k_fs_LR.surf.gii'*
> *R_template='standard.R.sphere.164k_fs_LR.surf.gii'*
>
> *wb_command -cifti-resample
> rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii COLUMN
> ${SUB}.curvature.native.dscalar.nii COLUMN BARYCENTRIC CUBIC
> ${SUB}.native.dtseries.nii \*
> *-left-spheres ${L_template} **${SUB}**.L.sphere.native.surf.gii \*
> *-right-spheres ${R_template} **${SUB}**.R.sphere.native.surf.gii*
>
> When I run this command, I get this note: *ERROR: left current sphere
> doesn't match input cifti*
>
> Is this the best command to use to resample the .*dtseries.nii to the
> native surface? If so, what is the correct current_sphere option to use?
> Also, the command asks for a cifti_template - what should I use here for
> the best native surface cifti template? I picked the curvature cifti
> because I wasn't sure.
>
> Please let me know what you think is the best way to get the resting-state
> surface data into native space!
>
> Thanks again,
> Jacob
>
> --
>
> Jacob Miller
> Graduate Student, D'Esposito Lab
> Helen Wills Neuroscience Institute (HWNI)
> University of California, Berkeley
>
> https://despolab.berkeley.edu/
>
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