Dear Doug, Thank you, this is very helpful! I had searched the web and the fs site extensively but did not find anything helpful on this problem before you rescued me.
I have some follow up questions: 1. Can the DeMeanFlag be used in qdec (qdec was segfaulting when doing similar analyses and presumably it is for the same reason) 2. When does correlations between covariates becomes a problem (e.g. 0.6 or 0.9) 3. When using dods, what are my options with somewhat correlated measures. I research brain changes in ageing. Typically I control for age, gender, icv, and sometimes other variables. In ageing, age, icv, and cognition tend to be correlated but it is critical to control, say, for icv to determine whether an effect of interest is due to women having on average smaller heads and therefore smaller brains or due to brain atrophy in some individuals, or to other factors. I really appreciate yours and your team's efforts both in developing great software and answering questions from challenged users like myself. Regards, Nic -----Original Message----- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 3/12/2008 5:34 AM To: Nicolas Cherbuin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit problem The problem is that there is a strong correlation in the two continuous variables due to their large non-zero means. The knee-jerk reaction is to simply demean the variables which is sometimes the right thing to do and sometimes not. In this case, I think it is ok because you are using DOSS. If you were to switch to DODS, it would be the wrong thing to do. Note, you can instruct mri_glmfit to demean the continuous variables by adding the following line to your fsgd file: DeMeanFlag 1 Again, you should be careful with this and don't use it with DODS doug Nicolas Cherbuin wrote: >Hi, > >I am analysing structural data with mri_glmfit. After pre-processing I have >first used one group variable (gender) with one covariate age. I had no >problem processing the data and visualising it in tksurfer. > >I then tried to add another covariate (measure of immediate recall). So I had >in total one group variable and two covariates. I reanalysed the data but got >the following error: > >FixVertexAreaFlag = 1 >UseMaskWithSmoothing 1 >OneSampleGroupMean 0 >y >/media/storage2/proc/freesurfer/60_w2/checked/analysis/lh.gender_age_immrec.thickness.10.mgh >logyflag 0 >usedti 0 >FSGD gender_age_immrec_fsgd.txt >glmdir lh.gender_age_immrec.glmdir >DoFFx 0 >Creating output directory lh.gender_age_immrec.glmdir >Loading y from >/media/storage2/proc/freesurfer/60_w2/checked/analysis/lh.gender_age_immrec.thickness.10.mgh >Matrix condition is 12866.7 >ERROR: matrix is ill-conditioned or badly scaled, condno = 12866.7 >Possible problem with experimental design: >Check for duplicate entries and/or lack of range of >continuous variables within a class. > 0.000 1.000 68.000 10.000; > 1.000 0.000 65.000 5.000; >[trunkated the fsgd file output but it is the same as the one used for the >sucessful analysis except for one extra column] > >After this error I thoroughly checked all my files but could not find anything >wrong. So to check I could do an analysis using the extra variable I did >another analysis with gender and immrec. This worked without problem. > >I have attached all my fsgd files and mat files. They all use the same >subjects and gender info and only differ by one column. Since permutations >worked I cannot fathom why it does not work when all put together. > >The mri_glmfit syntax used for each analysis was: > >mri_glmfit --y lh.gender_age_immrec.thickness.10.mgh --fsgd >gender_age_immrec_fsgd.txt doss --glmdir lh.gender_age_immrec.glmdir --surf >average100 lh --C gender_age_immrec.mat > >mri_glmfit --y lh.gender_immrec.thickness.10.mgh --fsgd >gender_immrec_fsgd.txt doss --glmdir lh.gender_immrec.glmdir --surf >average100 lh --C gender_immrec.mat > >mri_glmfit --y lh.gender_age_immrec.thickness.10.mgh --fsgd >gender_age_immrec_fsgd.txt doss --glmdir lh.gender_age_immrec.glmdir --surf >average100 lh --C gender_age_immrec.mat > >I use 4.01 (but also checked with 4.02) under Ubuntu 64 bit on a Xeon machine. > >Thanks very much for your help > >Nic > > > >------------------------------------------------------------------------ > >GroupDescriptorFile 1 >Class Male plus blue >Class Female circle red >Variables age >Input 60047 Female 68 >Input 60092 Male 65 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Female 65 8 >Input 63044 Female 65 9 >Input 63053 Male 67 5 >Input 63056 Male 66 6 >Input 63068 Male 66 8 >Input 63081 Female 67 8 >Input 63121 Male 65 7 >Input 63136 Male 65 7 >Input 63187 Female 67 7 >Input 63194 Male 65 6 >Input 63218 Male 67 6 >Input 63329 Female 67 4 >Input 63348 Female 66 8 >Input 63365 Male 68 7 >Input 63407 Female 66 8 >Input 63411 Male 67 7 >Input 63429 Male 66 9 >Input 63433 Female 65 5 >Input 63434 Male 65 8 >Input 63435 Female 68 8 >Input 63450 Female 68 6 >Input 63470 Male 68 6 >Input 63471 Male 66 8 >Input 63473 Male 67 8 >Input 63490 Female 68 9 >Input 63491 Female 69 6 >Input 63492 Male 68 6 >Input 63534 Female 64 12 >Input 63545 Female 65 6 >Input 63568 Female 69 10 >Input 63575 Male 66 5 >Input 63586 Female 67 5 >Input 63636 Male 65 7 >Input 63637 Male 66 5 >Input 63649 Male 66 10 >Input 63674 Female 69 8 >Input 63693 Female 65 12 >Input 63750 Female 65 7 >Input 63755 Female 68 8 >Input 63766 Male 66 6 >Input 63770 Male 67 6 >Input 63773 Male 65 4 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Female 64 7 >Input 64469 Female 68 8 >Input 64475 Male 64 7 >Input 64488 Female 66 7 >Input 64504 Male 68 7 >Input 64531 Female 64 6 >Input 64537 Female 64 6 >Input 64542 Female 65 8 >Input 64552 Female 67 11 >Input 64590 Male 66 3 >Input 64592 Female 68 7 >Input 64596 Male 66 9 >Input 64620 Male 69 9 >Input 64625 Male 67 7 >Input 64640 Male 64 8 >Input 64657 Female 66 6 >Input 64668 Female 66 4 >Input 64680 Male 66 7 >Input 64691 Male 67 7 >Input 64706 Male 69 4 >Input 64734 Male 67 4 >Input 64745 Female 66 7 >Input 64764 Female 66 7 >Input 64781 Male 66 10 >Input 64797 Male 66 7 >Input 64798 Male 68 7 >Input 64806 Male 67 8 >Input 64812 Male 66 7 >Input 64818 Male 66 9 >Input 64824 Female 65 6 >Input 64829 Male 67 8 >Input 64843 Female 67 9 >Input 64867 Female 68 6 >Input 64868 Male 68 7 >Input 64876 Male 68 5 >Input 64884 Female 68 7 >Input 64886 Male 69 6 >Input 64897 Female 68 10 >Input 64899 Male 65 4 >Input 64910 Male 65 6 >Input 64913 Female 68 12 >Input 64937 Male 68 5 >Input 64947 Female 65 9 >Input 64961 Female 68 8 >Input 64987 Male 67 11 >Input 64997 Male 68 5 >DefaultVariable age > > >------------------------------------------------------------------------ > > >$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ >cwd /media/storage2/proc/freesurfer/60_w2/checked/analysis >cmdline mri_glmfit --y lh.gender_age_immrec.thickness.10.mgh --fsgd >gender_age_immrec_fsgd.txt doss --glmdir lh.gender_age_immrec.glmdir --surf >average100 lh --C gender_age_immrec.mat >sysname Linux >hostname mri-lab >machine x86_64 >user u3184049 >FixVertexAreaFlag = 1 >UseMaskWithSmoothing 1 >OneSampleGroupMean 0 >y >/media/storage2/proc/freesurfer/60_w2/checked/analysis/lh.gender_age_immrec.thickness.10.mgh >logyflag 0 >usedti 0 >FSGD gender_age_immrec_fsgd.txt >glmdir lh.gender_age_immrec.glmdir >DoFFx 0 > > >------------------------------------------------------------------------ > >_______________________________________________ >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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
