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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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What to do after fitting pRF model? #230

Closed mwaskom closed 7 years ago

mwaskom commented 7 years ago

I've worked through the prerequisites for the t_pRF.m tutorial and have now successfully estimated a pRF model for Ernie.

However, while it was reasonably clear how to get to this point, thanks to the clear enumeration of the prerequisite tutorials in the header for t_pRF.m, I am at a loss for what to do next.

If I look in Gray/Averages I see a number of .mat files that seem relevant, but it's not clear from the tutorial what their contents are. For example, how does rmGaussian-gFit.mat differ from rmGaussian-fFit.mat, and how does that differ from rmGaussian-fFit-fFit.mat? Is there a guide to the outputs of the pRF model somewhere?

If I load one of these files and poke around, I see some fields that are probably relevant (x0, y0, sigmaMajor, etc. as vectors with a number of elements that I would expect for a single subject high resolution mesh). But many fields that don't have an obvious meaning. Is there a guide to the content of these files somewhere?

Mainly I would like to look at the results of the pRF model, and then I guess use them to define some ROIs in visual cortex. Are there tutorials for doing this? If I look in tutorials/mesh the only one that seems immediately relevant as an end goal is t_meshRetinotopy.m, but that turns out to involve the template model, not the pRF model I just estimated.

More broadly, I am aware that there is a GUI application that would probably help me answer some of these questions by poking around in various menus. But despite reading through the basics on the Vistasoft wiki and the tutorials up to pRF fitting, I don't believe I've been told how to open that application.

I offer these thoughts from the perspective of someone who has a broad sense of what I want to accomplish but is completely naive to the vistasoft library. The tutorials as written get me part of the way there, but not all the way.

mwaskom commented 7 years ago

Some of the information I am seeking can be found here: https://github.com/vistalab/vistasoft/wiki/mrVista

This page seems like the most relevant orientation for someone who wants to use mrVista for fMRI analysis, and provides some structure for understanding what is happening in the tutorials. It's currently not emphasized in the sidebar and is linked after the tutorials in the "Quick Links" but at least a condensed version of this information might be helpful on the "Getting Started" page (which currently just discusses Installation -- a necessary but not sufficient condition for getting started).

JWinawer commented 7 years ago

Yes, more tutorials are needed, including ones that do what you suggest. Happy to work with you to write a few new ones. Contact me offline if you want to do that.

On Tue, Apr 25, 2017 at 10:21 AM, Michael Waskom notifications@github.com wrote:

I've worked through the prerequisites for the t_pRF.m tutorial and have now successfully estimated a pRF model for Ernie.

However, while it was reasonably clear how to get to this point, thanks to the clear enumeration of the prerequisite tutorials in the header for t_pRF.m, I am at a loss for what to do next.

If I look in Gray/Averages I see a number of .mat files that seem relevant, but it's not clear from the tutorial what their contents are. For example, how does rmGaussian-gFit.mat differ from rmGaussian-fFit.mat, and how does that differ from rmGaussian-fFit-fFit.mat? Is there a guide to the outputs of the pRF model somewhere?

If I load one of these files and poke around, I see some fields that are probably relevant (x0, y0, sigmaMajor, etc. as vectors with a number of elements that I would expect for a single subject high resolution mesh). But many fields that don't have an obvious meaning. Is there a guide to the content of these files somewhere?

Mainly I would like to look at the results of the pRF model, and then I guess use them to define some ROIs in visual cortex. Are there tutorials for doing this? If I look in tutorials/mesh the only one that seems immediately relevant as an end goal is t_meshRetinotopy.m, but that turns out to involve the template model, not the pRF model I just estimated.

More broadly, I am aware that there is a GUI application that would probably help me answer some of these questions by poking around in various menus. But despite reading through the basics on the Vistasoft wiki and the tutorials up to pRF fitting, I don't believe I've been told how to open that application.

I offer these thoughts from the perspective of someone who has a broad sense of what I want to accomplish but is completely naive to the vistasoft library. The tutorials as written get me part of the way there, but not all the way.

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