As for your second question, the transform between MNINonLinear and
"Native" space (actually, undistorted, rigid registered) is a nonlinear
warpfield, not a 4x4 matrix (affine). As I recall, we ignore the 4x4
matrices in gifti surface files (.surf.gii), as they have caused more
trouble than good. To get a native-space surface, the best way is to start
with a native-space surface in the resampling, which are available inside
the T1w folder, rather than MNINonLinear.
Another terminology trap to warn of in advance: "native space" and "native
mesh" are completely unrelated concepts: "native space" means the volume
space, that is, what coordinates you will find an anatomical feature at.
"Native mesh" is just whatever topology (number of triangles and how they
are connected) comes out of freesurfer's segmentation and tessellation of
the surfaces - these concepts are orthogonal, we can and do provide (among
other things) native space fs_LR mesh surfaces, and MNINonLinear space
native mesh surfaces.
Tim
On Tue, Jan 15, 2019 at 8:33 AM Rigel Wang <
rigel.w...@neuroinformatics-collaboratory.org> wrote:
> Hi HCP team,
>
> Thanks a lot for your dedication to science.
>
> I am using your HCP-S900 dataset and Connectome Workbench for research.
>
> Specifically, in order to compare the E/MEG inverse solution, we are
> expecting to get the low resolution resting state fMRI on native space
> surface.
> We are trying to use HCP-S900 dataset for a test.
>
> For example, we want to downsample the
> *105923\MNINonLinear\Result\rfMRI_REST1_LR\rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii.*
>
> First, I use the wb_coomand -surface-resample in matlab to downsample
> the anatomical data(
> *system([wb_command, ' -surface-resample ',' ',file.highResSurface{hemi},'
> ',file.highResSphere{hemi},' ',file.lowResSphere{hemi},' ', res_method,'
> ',file.lowResSurface{hemi}]);) *for getting a low resolution suface which
> expecting to be around 3k vertices for each hemisphere. PS: downsampling
> the surface and projecting back to native space is for calculating the
> E/MEG leadfied.
>
> *Then I am trying to use the wb_coomand -cifti-resample for downsample the
> functional data(*
> *system([wb_command, ' -cifti-resample ',' ',file.highResCii,'
> ',res_src_direction,' ',cifti_templete,' ',res_template_direction,'
> ',res_surface_method,' ', res_volume_method,' ',file.lowResCii]);) . *
>
> *Question:*
>
> 1. I don't know what should I put in the <cifti_templete> for wb_coomand
> -cifti-resample?
>
>
> 2. Can I use the same project matrix from
> \105923\MNINonLinear\fsaverage_LR32k\105923.R.{pial or
> white}.32k_fs_LR.surf.gii file, which is 4*4 matrix, for projecting
> low-resolution 3k_fs_LR back, the output of -surface-resample, to
> individual native space?
>
>
> Thank you!
> Best,
> Rigel
>
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
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>
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