Hi,
I don't think this is an fslview error (fingers crossed) since it is not involved in processing steps that could lead to this bizarre looking all_FA. Superficially that image looks to be mis-registered… I'd look carefully at any registration stages going to your anatomical space… has any manual registration/resampling/reorientation been applied?
On 22 Mar 2013, at 04:35, Gabriel Gutfilen Schlesinger <[log in to unmask]> wrote:
> Dear FSL-users,
> i would like to ask you for your opinion.
>
> The result of a study including 66 controls and 113 pacients was that the whole brain skeleton has significant lower FA values in patients (with p<0.0001, everything appears yellow), that seem very strange to me.
>
> Trying to find out what happens:
> The index.html file shows apparently correct FA maps (http://img831.imageshack.us/img831/4897/slicedir.jpg)
> The order of the subjects in the origdata file is correct in relation to the design matrix.
> The nonlinear registration seems to be ok too, when looking to the individual FA_to_target maps.
> It seems that there is a problem with the visualization (see attached)? Strange is, when doing a time series on the all_FA map for example in the corpus calosum (http://img189.imageshack.us/img189/728/fslview.jpg) then the FA values seems to be projected correct (besides of some outliers).
> We are using 16Gb Memory 12 core Mac, that shouldn't be the problem.
>
> Can it be within the permuation process due to memory problems?
> Does somebody has an idea what could have happened?
>
>
> Attached slicedir index file
>
> Thanks in advance!
>
> Gabriel
>
--
Dave Flitney
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
URL: http://www.fmrib.ox.ac.uk/~flitney
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