To use the resulting dtseries.nii file with HCP data, you will first need
to map the cortical data to surfaces. The various -cifti-create commands
do not do this mapping, they are simply data conversion. You also need to
nonlinear register to MNI (for subcortical signal). The <label-volume> is
specifically to define the structures to represent as voxels in the
resulting dtseries file, which is why it says this about <label-volume>
lower in the help:
The label volume should have some of the
label names from this list, all other label names will be ignored:
CORTEX_LEFT
CORTEX_RIGHT
CEREBELLUM
ACCUMBENS_LEFT
ACCUMBENS_RIGHT
...
While that shows that it is possible to represent cortex as voxels in the
cifti format, note that it is not recommended, and that it is not what HCP
cifti files do (so you will have a very hard time using the HCP
parcellation unless you map your subject timeseries data to the surface).
The label volume for subcortical signal we use for HCP data exists in the
pipelines repository, the Atlas_ROIs.2.nii.gz file here:
https://github.com/Washington-University/Pipelines/tree/master/global/templates/91282_Greyordinates
The full process we use is fairly involved, and the HCP Pipelines (
https://github.com/Washington-University/Pipelines) are the easiest way to
do it, when you have data matching our acquisition recommendations. Even
if your acquisitions don't entirely meet our recommendations, many of the
pipeline scripts can still be used to make the process easier.
Tim
On Mon, Nov 14, 2016 at 3:11 PM, Guy Hwang <[email protected]> wrote:
> Hello,
>
>
> I am trying to turn nifti files into dtseries.nii so that I can later use
> -cifti-parcellate to create resting state connectivity matrices.
>
>
> 1) What is <label-volume>? As in the syntax "wb_command
> -cifti-create-dense-timeseries {output}.dtseries.nii -volume
> {input}.nii.gz <label-volume>"
>
>
> 2) Where can I find the most up-to-date dtseries.nii file from HCP to use
> for the parcellation?
>
>
> I would appreciate your help.
>
>
> Thank you,
>
>
> Guy
>
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>
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