Hi Yuko,
The contrast only allows you to constrain the anatomical ROI. If you don't spec a contrast, then it uses the whole anat ROI. Nothing gets averaged until you run funcroi-table-sess, and that only averages over the given contrast (unless you use -vol in which case it just reports the volume of the ROI from the previous stages). Make sense?
doug
Yuko Yotsumoto wrote:
Thanks Doug,
If I don't specify a contrast with funcroi-config, then, the value I get from funcroi-table-sess is the average across all conditions including fixation?
What I want to get is a non-thresholded value for each condition. So I should specify a contrast with funcroi-config, correct? And -c flag with funcroi-config requires -sign and -thresh. So, I guess I'm still stuck to my first question.
Q1) If I don't want to use any thresholding for ROI analysis, can I use "-sign abs -thresh 0" with funcroi-config?
What do you think? Yuko
On Dec 8, 2010, at 4:09 AM, Douglas N Greve wrote:
Good point! This is a slight bug in the program that it requires a contrast when you ask for the volume. This is because the volume is completely set once you run funcroi-sess, so it won't make a difference what contrast you specify. The contrast only matters when you ask it to report a mean of a contrast. So, you can just specify any contrast in your analysis, or you can download a new version:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/funcroi-table-sess
I've updated the docs for this one as well.
thanks
doug
Yuko Yotsumoto wrote:
Thanks Doug,
On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote:
I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Q1) If I don't want to use any thresholding for ROI analysis, can I use "-sign abs -thresh 0" with funcroi-config?
Even easier: just don't specify a contrast.
Let me clarify. I can run funcroi-config without a contrast, but funcroi-table-sess requires one. Does this mean I don't specify a contrast with funcroi-config, but use -c with funcroi-table-sess gives all values within the label?
Yuko
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