Hi Freesurfers
Sorry for my previous email today (see below), I found a bug in my SPM code.
Now, the fsig.nii image works fine and does the job.
However, I have some additional questions:
1. Is there a way I can change the colour specification for rtview e.g.
swapping red and green colours?
2. Is there any smoothing applied by rtview? If yes, how much?
3. Does rtview use any significance threshold (e.g. p=0.05) to depict the
overlay? Can it be adjusted manually or I am expected to put already
thresholded data into the fsig image?
4. If I adjust the colorbar in the configuration, then it changes the
appearance of the colorbar, but not the colours on the figure. On the other
side, it seemingly changes the threshold of what fsig values should be depicted
on the figure or not. Is it meant to be that? I thought that the colorbar
represents the colorwheel and I also read in a freesurfer discussion, that its
values are in radian.
Your help is really appreciated.
Thanks a lot and best
Agoston
Date: Thu, 27 Aug 2015 12:08:32 +0000
From: Agoston Mihalik <axm...@student.bham.ac.uk>
Subject: [Freesurfer] fsig.nii with rtview
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<3aa2307d7caddc4d9e41a6fe348eafd3b6f28...@ex10.adf.bham.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Dear Freesurfers
I started using rtview to be able to delineate regions in my retinotopy data,
however, I ran into problem with the fsig.nii file. I do my analysis in SPM, so
I create the sine, cosine and significance images there as follows:
The sine and cosine images are regressors (parametric modulators) in the GLM.
They seem to be all right, and I get nice revearsals in tksurfer using the RYGB
wheel and complex display option.
I generated an F-contrast (sine and cosine activations different from
baseline), then calculated significance values myself knowing the degrees of
freedom. I also converted the values to -log10 scale. Now, if I use this images
with rtview, I get sparse activations across the brain and almost nothing in
the visual regions.
Interestingly, if I use the F contrast image (including F values) as fsig.nii,
I get nice activations and reversals in the visual regions (and many also
elsewhere), however, I think that's not the way I should do.
Can someone help me what I am doing wrong?
Thanks a lot!
Best
Agoston
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