Hi -yes sounds like you need to make sure the output of fsl_glm is ok. If you have columns in the design matrix that only have one nonzero value then you expect the corresponding volume to be empty in the output
Cheers
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington,
Oxford. OX3 9 DU, UK
+44 (0) 1865 222726 (fax 222717)
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http://www.fmrib.ox.ac.uk/~steve
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On 2 Oct 2011, at 03:53, Debby Klooster <[log in to unmask]> wrote:
> Thank you very much for the responses.
> So just to confirm that I'm doing the right thing:
> fsl_glm -i (nifti file) -d (.txt file with the confounds) -o nifti_betas.nii --out_res=nifit_confoundCorrected.nii
>
> I use the nifti_confoundCorrected as input for my ICA analysis in MELODIC. The results are not completely concordant with my expectations. When I look at the nifti_confoundCorrected with FSL view, a lot of volumes look completely white or completely black. Should I edit my confounds before performing confound correction (whitening and demeaning) before applying the confound correction? I cannot find a clear answer in literature about that.
>
> Thank you,
> Debby
>
>
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