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vistalab / vistasoft

VISTASOFT is the main software repository of the VISTA lab at Stanford University.
http://vistalab.stanford.edu
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Export ROI for use in SPM #299

Closed welbourne closed 3 years ago

welbourne commented 6 years ago

Hi everyone

A colleague of mine wants to make use of the mrVista tools for running pRF/retinotopy analysis on sweeping bar stimuli. The rest of their data is processed in SPM, and they'd like to be able to define ROIs within mrVista and then use those in their other pre-existing analysis.

What is the process of exporting ROIs defined in mrVista into a format that is readable in SPM (and is aligned properly)?
I see that there is an roiSaveAsNifti function - would that be all that is needed to run before importing into SPM, or are there other associated steps?

Any tips would be greatly appreciated.

Kind regards Lauren

JWinawer commented 6 years ago

I haven’t used spm, but that function should save out a volumetric nifti with the same header as the t1. The nifti will be a binary mask, with 1s for voxels in the ROI. I would guess that’s a pretty generic format readable by mist software tools.

On Tue, Jul 24, 2018 at 6:13 PM welbourne notifications@github.com wrote:

Hi everyone

A colleague of mine wants to make use of the mrVista tools for running pRF/retinotopy analysis on sweeping bar stimuli. The rest of their data is processed in SPM, and they'd like to be able to define ROIs within mrVista and then use those in their other pre-existing analysis.

What is the process of exporting ROIs defined in mrVista into a format that is readable in SPM (and is aligned properly)? I see that there is an roiSaveAsNifti function - would that be all that is needed to run before importing into SPM, or are there other associated steps?

Any tips would be greatly appreciated.

Kind regards Lauren

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welbourne commented 6 years ago

Great, thanks for the quick reply!

I'll update in a couple of weeks to confirm if it worked, for others' info.

marco-create commented 3 years ago

A few years later, I have the same need to convert ROI to nifti and I can confirm that roiSaveAsNifti works like a charm. Thanks! I guess, you can close this issue.