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Hello,
thanks for your report. Please see my responses below.
Best,
Kersten
On Thu, 2023-11-02 at 12:44 +0000, yildirim adalioglu wrote:
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> External Email - Use Caution
> To whom it may concern,
>
> Hello! We are currently trying to do a ST-LME (Spatiotemporal-LME)
> analysis based on bipolar disorder brain MRI images. We are having 2
> problems:
>
> 1)In the lme_mass_fit_EMinit step, we get a warning that says matrix
> is singular, close to singular or badly scaled.
>
> 2)In the lme_mass_RgGrow step, it says "computing seeds" indefinitely
> and it never ends.
>
> We looked for people having similar problems, however we could not
> find a solution. Currently, we suspect that this may be due to the
> zeros in the columns of fs_read_Y('lh.thickness_sm10.mgh').
Zeros in the data variable ('Y') should be OK if they are masked by the
'lhcortex' or 'rhcortex' mask. This should be a list of indices where
the data is not zero. Could you check if this is the case?
Alternatively, such errors could possibly occur due to the design
matrix specification. The matrix should not contain columns that are
redundant (for example, do not include an intercept and, in a two-group
scenario, variables for both group 1 and group 2). Could you also check
for such issues (or maybe briefly describe how your design matrix looks
like)?
Thanks.
> Do you happen to know the reasons of these problems? Thank you for
> your time.
>
> Sincerely,
> Yıldırım Adalıoğlu
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