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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1AHsPBJ6fOJADbOsf7invI8gM0i-BVGQhx0_Ic5e088gwUT... Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.