Question regarding export of parcellated atlas volumes in DSI Studio

[Jaiprakash Gurav]

Dear DSI Studio Team,

I hope you are doing well.

I am currently using DSI Studio for preoperative planning and research applications, particularly for cortical surgery. I see that DSI Studio provides access to multiple human atlases that can be used for cortical parcellation as well as thalamic nuclei segmentation, which has been very helpful.

However, I am running into an issue during export. When I export the volumes and generate a NIfTI (.nii) output, the exported file does not appear to contain the atlas parcellation labels (i.e., the parcel-level segmentation is not preserved in the NIfTI file). Instead, it seems to export only the underlying volume without the parcellated regions.

I wanted to ask:

• What is the correct workflow to export atlas-based parcellations (cortical or thalamic) as labeled NIfTI files?

• Is there a specific export option or setting that ensures the parcellation labels are retained?

• Alternatively, is there a recommended way to convert or save these parcellations for use in external software (e.g., for volumetric analysis or surgical planning)?

I would appreciate any guidance or documentation you could share on this.

Thank you very much for your time and for developing such a powerful tool.

Best regards,
Jaiprakash Gurav

[Frank Yeh]

Sorry for my delayed reply:

>
> However, I am running into an issue during export. When I export the volumes and generate a NIfTI (.nii) output, the exported file does not appear to contain the atlas parcellation labels (i.e., the parcel-level segmentation is not preserved in the NIfTI file). Instead, it seems to export only the underlying volume without the parcellated regions.

You may need to use [Save checked regions into one 3D NIFTI]

>
> Alternatively, is there a recommended way to convert or save these parcellations for use in external software (e.g., for volumetric analysis or surgical planning)?

The save as above.

Best regards,
Frank