External Email - Use Caution Hi,
Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify? Thanks again, Colleen On 2018-04-30 14:43, C.P.E. Rollins wrote: > I thought that I could not remove the class since this would mean that > the contrast positive and negative values would no longer add up to 0. > For instance if I remove only class "patient_centre2_female", then my > contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could > you please clarify? > > Thanks again, > Colleen > > -------- Original Message -------- > Subject: Re: [Freesurfer] FSGD design for multi-centre study > Date: 2018-04-20 11:19 > From: "C.P.E. Rollins" <cp...@cam.ac.uk> > To: Freesurfer <freesurfer@nmr.mgh.harvard.edu> > > Thanks a lot for the explanation. The issue is that I don't think > Freesurfer will run a design for which there are no subjects for a > given class. So if I keep the classes (24 classes since 6 centres x 2 > gender x 2 groups (patient vs. control), and have the contrast with 12 > (-1) and 12 (1), > -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 > I get the error: > -------------------------------- > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > -------------------------------- > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > > I'm assuming this is because there are no participants in, for > example, patient_centre2_female > Is there any way to get around this issue, or should I remove those > centres from my analysis (since I can't only remove > "patient_centre2_female", as this would make the contrast unbalanced > (positives and negatives would not add to the same number). I hope > this was clear but please let me know if it was not. > > Thanks again, > Colleen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
