Hi Ed, permuting the matrix will not help. The problem is that some weighted combination of columns is equal to some other column. It means thatsome of your covariates are highly correlated. Sometimesthis is obvious (eg, two columns are the same), other times it is very subtle. You will need to look carefully at your covariates to see if some are correlated. This might be a mathematical examination, but it could also be qualitative (eg, age and weight in children will correlate). Sorry I can't give you more guidance. doug
On 02/27/2013 11:24 AM, Ed Gronenschild wrote: > Hi Doug, > > Can I do this by just permuting the contrast matrix and the > corresponding columns > in the fsgd file? > > Ed > > On 26 Feb 2013, at 17:43, freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > > Hi Ed, I think it is just the way you have the matrix set up. You'll > need to alter the matrix in some way. > doug > >> Message: 7 >> >> Date: Tue, 26 Feb 2013 10:08:07 +0100 >> >> From: Ed Gronenschild <ed.gronensch...@maastrichtuniversity.nl >> <mailto:ed.gronensch...@maastrichtuniversity.nl>> >> >> Subject: Re: [Freesurfer] Problem with glmfit: matrix is >> >> ill-conditioned >> >> To: "freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>" >> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> >> Message-ID: >> >> <2031202f-e366-48cb-82a9-3142378ad...@maastrichtuniversity.nl >> <mailto:2031202f-e366-48cb-82a9-3142378ad...@maastrichtuniversity.nl>> >> >> Content-Type: text/plain; charset="us-ascii" >> >> >> Hi Doug, >> >> >> The condition numbers were: >> >> - 1e+08 for problematic fsgd file >> >> - 371.233 for previous fsgd file >> >> >> I tried also v5.1, however with no succes. The matirx was still >> >> ill-conditioned with condition number 2.80809e+07. >> >> >> Cheers, >> >> Ed >> >> >> On 1 Feb 2013, at 9:53, freesurfer-requ...@nmr.mgh.harvard.edu >> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >> >> >>> Message: 12 >>> >>> Date: Thu, 31 Jan 2013 14:08:11 -0500 >>> >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@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: <510ac11b.4090...@nmr.mgh.harvard.edu >>> <mailto:510ac11b.4090...@nmr.mgh.harvard.edu>> >>> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> >>> >>> 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 columns1 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 <gr...@nmr.mgh.harvard.edu >>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>> >>>>> <mailto:gr...@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> >>>>> >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>> >>>>> Message-ID: <5101749b.4060...@nmr.mgh.harvard.edu >>>>> <mailto:5101749b.4060...@nmr.mgh.harvard.edu> >>>>> >>>>> <mailto:5101749b.4060...@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: >>>>>> >>>>>> 1. 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 >>>>>> >>>>>> >>>>>> 2. The FSGD file (if using one) >>>>>> >>>>>> 3. 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 >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> >>>> Freesurfer mailing list >>>> >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> -- >>> >>> Douglas N. Greve, Ph.D. >>> >>> MGH-NMR Center >>> >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> >>> Phone Number: 617-724-2358 >>> >>> Fax: 617-726-7422 >>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ >>> >>> greve/ >>> >> >> -------------- next part -------------- >> >> An HTML attachment was scrubbed... >> >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130226/f8558727/attachment-0001.html >> >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
