As long as the volume tab is view yoked, and the "move to identified
location" button is enabled, yes (both of these have preferences as to
whether they are the default, but the initial preference setting is to have
them enabled by default). The mm coordinates will be the same, surface or
volume (with rounding-like error for finding the nearest voxel center), the
volume tab is only required if you want the voxel indices (which are
specifically from the lowest volume layer that is enabled). If you only
need mm coordinates, then you don't need to switch tabs, the identification
window will show the coordinates of the nearest vertex to your click.
If you want to specifically identify coordinates on the skull near specific
surface features, you may want to make use of the volume tab - there is an
oblique mode where you can rotate the slices to approximate the closest
point on the skull. However, please double check any coordinates obtained
from oblique mode, as it hasn't been tested as thoroughly (and has had some
quirks in the past). Orthogonal mode and "All" view, and toggling the
slices on and off, may be useful in checking the coordinates.
You will, of course, need a way to transfer those coordinates back to the
actual subject for stimulation, since as recently discussed, the T1w
coordinates are not the original scanner coordinates, but distortion
corrected, rigidly-registered coordinates.
Tim
On Thu, Feb 14, 2019 at 11:34 AM Somers, David <som...@bu.edu> wrote:
> We are attempting to define brain stimulation coordinates in native volume
> space based on an analysis performed on individual subject functional data
> preprocessed using the HCP preprocessing pipeline. We think we have figured
> out how to do this correctly, but would greatly appreciate confirmation or
> correction.
>
> Our understanding is that if we are only interested in locations within
> the cortical ribbon we do not need to perform any resampling and we can
> simply load the results along with the surfaces and volumes located in
> ${Subject}/T1w/.
>
> wb_view
> ${SubjectFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.32k_fs_LR.wb.spec
> func.dscalar.nii
>
> Now if we select a point on the surface (e.g.
> ${Subject}.R.midthickness.32k_fs_LR.surf.gii) we should be able to go to
> the Volume tab and get voxel coordinates of the corresponding point in
> native volume space. Is this correct?
>
> Thanks in advance for your answer.
>
> David C. Somers, Ph.D.
> Professor & Chair
> Dept. of Psychological & Brain Sciences
> Boston University
>
>
>
>
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
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