Dear Mark,

Thank you! I was hoping there would be a way to view the statistical image in the standard FSL software package, but I guess that's not the case then?

All my best,
Lizanne

 

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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Tuesday, January 26, 2016 12:03 AM
To: [log in to unmask]
Subject: Re: [FSL] fslview: statistical images in the 3D-viewer

Hi,

To see things in as a 3D rendering you need to follow the instructions on the wiki:

  http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide#Viewing_results

Especially the bit about downloading and running the first3Dview script.

All the best,

Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Schweren, Lizanne" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, 25 January 2016 23:58
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] fslview: statistical images in the 3D-viewer

Dear FSL experts,

I’m trying to visualize a statistical image of the surface of the hippocampus (resulting from first_utils and then PALM) in the FSL 3D viewer. I can’t get the statistical

values to be displayed. I’ve attached a screenshot of what I get, with the following steps:

--> open a standard brain

--> add the statistical image I want to display (c1_sub1_abs)

--> change the settings of my statistical image to 'statistic' type, and 'Red-Yellow' color

--> change the threshold of my statistical image to min=0.95 and max=0.999 (they are inverted p-values)

--> open the 3D viewer, and turn off the standard brain

In the normal viewer, I see what I want to see, i.e. a gradient. However in the 3D viewer

on the right I don’t get gradients, just orange. Playing with the thresholds makes the orange surface larger or smaller, but it does not give me gradients. What am I doing wrong? Thank you very much again for your help!

All my best,

Lizanne