External Email - Use Caution Thanks a lot Doug. Normalizing the age worked out.
Regards, Nabin On Tue, Aug 14, 2018 at 5:29 PM Douglas Greve <dgr...@mgh.harvard.edu> wrote: > The main problem is the 4th group where you only have two subjects and > they are almost exactly the same age. This makes it hard to estimate the > age slope and is causing the ill-conditioned error. You can try normalizing > the ages (ie subtract the mean and divide by the stddev), you can remove > age as a covariate, you can eliminate this group. Alternatively, you can > elimate the age slope just for this group (this requires that you create > your own design matrix). > > On 8/14/18 6:00 AM, Nabin Koirala wrote: > > External Email - Use Caution > Hi freesurfer community, > > I am trying to do QDEC with a data for 2 groups but stuck in this error > for many hours now. Tried and checked everything I could think of. Also > went through the old threads and checked those recommneded but still could > not solve it. Your hint will be very helpful. > > *ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1* > *--------------------------------* > *Possible problem with experimental design:* > *Check for duplicate entries and/or lack of range of* > *continuous variables within a class.* > *If you seek help with this problem, make sure to send:* > * 1. Your command line:* > * mri_glmfit --y > /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd > /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods > --glmdir /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled --surf > fsaverage lh --label > /gpfs/fs1/home/mmuthura/freesurfer/subjects/fsaverage/label/lh.aparc.label > --C > /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > --C > /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-f-m-Intercept-thickness.mat > --C > /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-Epi-Chr-Intercept-thickness.mat > --C > /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-X-gender-Group-Intercept-thickness.mat* > > *2. The FSGD file (attached)* > > *3. Design Matrix* > > Design matrix ------------------ > 1.000 0.000 0.000 0.000 31.300 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 22.760 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 29.390 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 49.160 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 23.810 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 45.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 21.830 0.000 0.000; > 1.000 0.000 0.000 0.000 49.540 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 40.550 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 22.660 0.000 0.000; > 1.000 0.000 0.000 0.000 26.080 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 32.570 0.000 0.000; > 0.000 1.000 0.000 0.000 0.000 47.190 0.000 0.000; > 1.000 0.000 0.000 0.000 27.710 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 25.860 0.000 0.000 0.000; > 1.000 0.000 0.000 0.000 25.180 0.000 0.000 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 27.630 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 51.930 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 25.060 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 60.650; > 0.000 0.000 1.000 0.000 0.000 0.000 59.360 0.000; > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 62.450; > 0.000 0.000 1.000 0.000 0.000 0.000 20.480 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 36.550 0.000; > 0.000 0.000 1.000 0.000 0.000 0.000 37.000 0.000; > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. >
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