We are going to need a bit more information than that, I don't know what
you mean by "subcortical data is not separated from the surface", do you
mean that the cortex data is represented in voxels in the cifti file also?
You should be using the -left-metric and -right-metric options for the
surface data (and -roi-left and -roi-right options to exclude the medial
wall), and -volume with a label volume that has only the subcortical labels
of interest in it, that is, it should not have CORTEX_LEFT and CORTEX_RIGHT
labels (unless you want the cortex data to be represented as voxels also).
If you want to do comparisons between it and the HCP released data, you'll
likely want to use the medial wall rois and label volume that we use for
our grayordinate space, rather than files derived from the subject. The
surface ROIs can be retrieved from an existing HCP cifti file with
-cifti-separate using the -metric and -roi options. The volume label file
exists in HCP subject directories (I don't know if it exists somewhere else
also), here:
${StudyFolder}/${SubjectID}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
Tim
On Fri, Feb 27, 2015 at 5:53 PM, Marta Moreno <[email protected]>
wrote:
> Hi users,
>
> I am working on 7 T data doing some testing for fc analyses and would like
> to to create a cifti file from nifti1 (my nifti1 fc t-map was created with
> SPM).
>
> I am using wb_command -volume-to-surface-mapping and wb_command
> -cifti-create-dense-scalar to have my cifti file but when loading into
> workbench my subcortical data is not separated from my surface t-map.
> What am I doing wrong?
>
> Thanks,
>
> Leah
> _______________
> Marta Moreno-Ortega, Ph.D.
> Postdoctoral Research Fellow
> Division of Experimental Therapeutics
> New York State Psychiatric Institute
> Department of Psychiatry
> Columbia University College of Physicians and Surgeons
>
>
>
>
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>
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