Dear HCP experts,
I am interested in mapping individual voxels in a subject's FreeSurfer
conformed space (orig.nii) onto the HCP template (fsaverage_LR) while
maintaining the original voxel values.
All of the voxels lie within the LH cortical ribbon in the (conformed)
volume space. There are 186 voxels with non-zero values that act as unique
identifiers, with all other voxels having a value of zero.
I have prepared the native FreeSurfer to HCP transformations, then
performed volume-to-surface mapping of the sample data, and finally applied
the FreeSurfer-to-HCP transform to the sample data. I have tried to
identify the options that perform something like Nearest Neighbour
assignment, as I need to maintain the original values as identifiers. The
problem I am facing is that volume-to-surface mapping as done below reduces
the number of non-zero voxels/vertices from 186 to 94, and the
Freesufer-to-HCP resampling reduces the number of non-zero vertices further
from 94 to 13 non-zero points.
I would greatly appreciate your guidance as to the best way to achieve my
desired goal of obtaining all 186 vertices with their original values onto
the HCP template. Should I map each voxel to the closest voxel on the
FreeSurfer WM surface, or something similar?
The commands I used are shown below.
Many thanks,
Sean
wb_shortcuts -freesurfer-resample-prep lh.white.surf.gii lh.pial.surf.gii
lh.sphere.FSave.reg.surf.gii
HCP_S1200_GroupAvg_v1/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
lh.midthickness.surf.gii
${current_subject}.l.midthickness.32k_fs_LR.surf.gii
lh.sphere.HCP.reg.surf.gii
and then created a volume-to-surface mapping, while maintaining the
original voxel/vertex values using
wb_command -volume-to-surface-mapping '
{current_subject}_samples_LH_cortex.nii.gz
lh.midthickness.surf.gii samples_native.shape.gii -enclosing
and then applied the transform using
wb_command -metric-resample samples_native.shape.gii
lh.sphere.HCP.reg.surf.gii
HCP_S1200_GroupAvg_v1/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
BARYCENTRIC -largest {current_subject}_samples_HCP.shape.gii
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
