Help with flattening and mapping segmentation to fMRI data

[Johanna Schrader]

Hi!

I want to flatten the fMRI data to 2D images and map the data with the Brain/MINDS reference brain atlas (https://dataportal.brainminds.jp/atlas-package-download-main-page) or some similar segmentation. Then I want to extract the values from those segments. I want to automate this to get the data from a complete data set. 

Trying to map the Brain/MINDS atlas on the HCP data results in an error with a mismatch for voxels (Surface file contains 167082 vertices but the CortexRight contains 163842 vertices.) Can you explain, how can I map such a flattened segmentation?

I cannot find an option to export data from the connector workbench and as ideally I would want to run a script processing a full data set in the described manner, can you name a tool I can use to implement such a script? 

The wb_command is not working for me and I expect, this is intended to perform such a task? Are there any alternatives?

Thanks in advance!

Kind regards,

Johanna 

[Tim Coalson]

To transfer data from one surface mesh to another, you need a surface registration between them.  The way workbench expects surface registrations to be represented is with a pair of spherical surface files.  Once you have them, you can use wb_command -metric-resample or -cifti-resample to resample the data onto the other surface mesh, depending on the format.

Brain/MINDS appears to be a marmoset atlas, not a human atlas.  Cross-species registration is challenging due to the amount of evolutionary cortical expansion and needing to choose appropriate features that are plausibly conserved, and is still an area of active development.

Tim

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/A71552AF-5C6D-40B9-8C4E-DB1296EE49DF%40l3s.de.