[pymvpa] question about detrend and zscore

[John Clithero]

Hi,

Looks like my email with the voxel image is waiting for moderator
approval, so here is my updated response without the picture:

On Tue, Oct 6, 2009 at 4:39 PM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
> On Tue, 06 Oct 2009, John Clithero wrote:
>> The 'wb_file' is func data with the relevant timepoints... it has had
>> some preprocessing done in FSL (motion correction, slice timing, brain
>> extraction). The ROI mask is a whole brain mask. It seems (I hope)
>> that the NiftiDataset is being put together correctly.
> wild guess - may be while doing FSL preprocessing you've done some
> intensity normalization?
Here (sorry if I didn't list them) are the preprocessing options I used in FSL
(1) brain extraction
(2) motion correction
(3) slice-timing correction
(4) high-pass filtering
Added this just now:
As far as I know, FSL does the following (from website and their
course lectures):
"Scale each 4D dataset by a single value to get the overall 4D mean
(dotted line) to be the same"
The intensitiy normalization was off during preprocessing (as FSL recommends).
Is this what you were asking about?

>
>
>> This perfect negative correlation occurs even if I feed in arbitrary
>> labels to the NiftiDataset, so there must be some sort of error in how
>> I'm using detrend and/or score?? I am guessing this is my erros since
>> the raw feature data looks fine to me.
>
>> This perfect negative correlation also occurs after just implementing
>> "zscore" or "detrend", although obviously the values are different.
> so, they aren't present in just loaded dataset but if you do zscore or
> detrend -- they come?

If I break data in half (A trials vs B trials, or random) before using
zscore or detrend, I generally see strong positive correlation (some
voxels are just more active than others across the experiment...this
makes sense).  But, once I use zscore or detrend....then goes to
perfect negative correlation (when looking at meanA vs meanB).
Each voxel after zscore, as it was said early, will have a mean of
zero across all trials...this is true for all the voxels.

>
> could you just plot 1 voxel (which later carries perfect correlation)
> before/after detrend?
>
This is waiting for moderator approval, I guess.
Thanks for the help.

Cheers,
John


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