Dear Helmut,
Thanks for yor response.
I've no experience in working with Marsbar tool. Sorry if I'm troubling
with silly doubts.
My research interest is as follows:
I'm doing a fmri ( language paradigm) study in schizophrenia and healthy
controls.
My research focus is to extract percent signal change from each individuals.
My research hypothesis: I'm expecting a lowered % signal in broca's area
(inferior frontal gyrus-ROI) of patients compared to controls.
I've done the folo. steps.
Preprocessed the images: Segmentation(T1W image). Normalize: write. Realign
and unwarp. Coregister: Estimate. Normalize: write. Smooth
1st level analysis
Contrast images were generated.
Open marsbar
ROI definition>> get spm cluster> selected the spm.mat (obtained after
second level analysis: 1 sample t test for 21 controls-contrast images were
used)
Then parameter extraction were done and got the folo. values.
1.1051 0.6977
1.2239 0.9895
0.3092 0.4176
0.8016 0.3438
0.9381 0.8560
0.2588 -0.0930
0.5137 0.2713
0.0161 0.2151
0.2973 0.5605
0.3460 0.3824
1.3272 1.2018
0.6188 0.6027
0.1151 0.3892
0.3955 0.3778
0.5390 0.4361
0.5888 0.2432
0.6467 0.6060
0.6153 0.5077
0.8178 0.8533
0.6397 0.7594
0.6046 0.2852
In this context, I had 2 ROIs.,
From your explanaton I understand that 6th control subject is showing
reduced activation with respect to the task. Am I right?
Now I wanted to calculate the percent signal change. There window is asking
for Duration?
What should I enter. Is it the TR value which I use?.
Thanks in advance for your response.
On Mon, May 12, 2014 at 7:15 PM, Helmut Nebl <
[log in to unmask]> wrote:
> Dear Amy,
>
>
> not sure whether you extracted beta/contrast estimates or percentage
> signal change. In any case, it's difficult to tell whether something is a
> "good variation" or not except you have a clear hypothesis about the
> values. There might be very small but highly consistent and/or highly
> significant differences between conditions.
>
> Negative values mean that there's a negative correlation with the expected
> BOLD response or a negative percentage signal change, which corresponds to
> a reduced activation or a deactivation, depending on context/contrast. If
> your rows correspond to different subjects, then there's one subject who
> shows reduced activations in the 2nd ROI. That's it. There might be various
> reasons, e.g. due to anatomical or functional variability the activation
> peak for that subject might fall outside of the ROI, alternatively that
> subject might just not recruit this area at all. See it as variability
> between subjects. In general it's no reason for subject exclusion. Values
> above 1 just mean the beta/contrast estimates or the percentage signal
> change is larger than 1. The range is not resticted to 0 - 1 (or -1 to 1).
> Again, in general this is highly variable between subjects.
>
> Of course you can check the data quality (e.g. look at the mean EPI
> volume, is there signal loss in that particular region due to
> susceptibility artefacts, check the motion parameters and their correlation
> with particular conditions), but you should do so for all of your subjects,
> as any value, whether positive or negative, could trace back to some
> artefact.
>
>
> Hope this helps,
>
> Helmut
>
>
