Hi Ed, that sounds strange. What were the condition numbers for the two analyses? This should be printed out into the terminal. It is also possible that it is a scaling issue. This should not be an issue in 5.1, but it is possible that it could have an effect if two columns are very similar. doug
On 01/30/2013 05:10 AM, Ed Gronenschild wrote:
Hi Doug,
It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went well. So probably some other columns are highly correlated as well. Anyway, what can we do about it? Just leave the offending covariate(s) out?
Cheers, Ed
Message: 1 Date: Thu, 24 Jan 2013 12:51:23 -0500 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5101749B.4060305@nmr.mgh.harvard.edu mailto:5101749B.4060305@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ed, the problem is that your covariates are highly correlated. Eg, column 1 is nearly identical to column 17. doug
On 01/24/2013 06:36 AM, Ed Gronenschild wrote:
Hi,
Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following error message:
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. If you seek help with this problem, make sure to send:
- Your command line:
mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh --fsgd../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/fsgd_sib_con_cann_aangepast3.fsgd dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf fsaverage lh --C ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/group_thickness_gender_scan_age_educ_hand_cann.mtx
- The FSGD file (if using one)
- And the design matrix above
Please find attached the requested files.
I noticed that rows 68 and 147 of the matrix Xg.dat are identical, and most probably caused the error. In the fsgd file I see that the correspondig cases indeed have identical values, although they are referring to different data. How to proceed?
Cheers, Ed
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