Hi Matt,

Than you for your explanation.
Now I've done surface mapping and resampling to a lower resolution standard mesh (32k) of fMR data using -surface-average, -volume-to-surface-mapping, and -metric-resample.

Then, I'd like to subcortical processing for 4D fMR data.
May be, I have to resample subcortical time series from individually defined greymatter nuclei to atlas defined nuclei, resulting in a standard set of subcortical voxels.
According to help "wb_command -volume-parcel-resampling <vol-in> <cur-parcels> <new-parcels> <kernel> <volume-out>", I'd like to type a command script like below,
Sigma = 2
wb_command -volume-parcel-resampling fmcpr.up.nii wmparc.nii.gz <new-parcels> $Sigma R_thalmus.nii -subvolume 10

What I don't know is,
1) "wmparc.nii.gz" in mri directory of freesurfer result is the <cur-parcels> or not?
2) what is the <new-parcels> and how can I produce <new-parcels> file before performing the script above?
3) Is it correct "-subvolume 10" for right thalamus? (when the value of label in wmparc.nii.gz is 10 for right thalamus)
4) if so, there any way to make all <volume-out> files (thalamus, caudate, putamen ..... ) at once?

Thanks,

Jeong

--------
I do struggle a bit when the previous e-mails in a thread are not included
below.  You always want to be mapping data to the midthickness surface
(which you can create by averaging the white and pial surfaces with
wb_command -surface-average.  Your output will be the <filename>.func.gii
metric file containing the timeseries for one hemisphere (so you¹ll need
to get the other one from the other hemisphere).  Ribbon-constrained
mapping takes the white and pial surfaces, not the ribbon NIFTI file.

Peace,

Matt.

On 4/29/14, 1:10 AM, "SUBSCRIBE FSL B. Jeong" <[log in to unmask]> wrote:

>Hi Matt,
>
>Thank you for your kind explanation.
>Unfortunately, I'm a newbie in terms of wb_command.
>Could you kindly explain for me?
>
>If I have a 4D fMRI file ("fMR.nii.gz"), two freesurfer pial files
>("lh.pial.gii", "rh.pial.gii"), and two freesurfer ribbon files
>("rh.ribbon.nii.gz", "lh.ribbon.nii.gz"), what is the correct wb_command
>script for mapping from fMR to surface space?
>
>The script below produced error message.
>
>wb_command -volume-to-surface-mapping fMR.nii.gz lh.pial.gii
>output.dtseries.nii -ribbon-constrained lh.ribbon.nii.gz
>
>If -ribbon-constrained is replaced -trillinear, "output.dtseries.nii" was
>produced. But workbench was not able to read it.
>
>Thanks,
>
>Jeong
---------

The exact process described in Glasser et al 2013 is a bit long as well
and relies on previous pipelines for some things.  The basic idea is
volume to surface mapping with a ribbon-based approach (i.e. Define grey
matter as the portion of voxels between the white and pial surface):

wb_command -volume-to-surface-mapping

Resampling to a lower resolution standard mesh (using a registered native
mesh sphere), in this case a 32k mesh with 2mm average vertex spacing.

wb_command -metric-resample

Subcortical timeseries are resampled from individually defined grey matter
nuclei (e.g. the thalamus) to atlas defined nuclei (making use of a prior
nonlinear volume registration to achieve alignment), resulting in a
standard set of subcortical voxels.

wb_command -volume-parcel-resampling

Then the standard surface data and standard subcortical data are combined
into a dense timeseries

wb_command -cifti-create-dense-timeseries

Peace,

Matt.