Hi Doug, This is the complete terminal output:
cwd /SA cmdline mri_glmfit --y /FREESURFER/lh.thickness.15.mgh --fsgd SA_base.fsgd --C /FREESURFER/con4.mtx --surf fsaverage lh --cortex --glmdir /FREESURFER/lh.pair-thick-T1-00.glmdir --pvr /FREESURFER/lh.paired-cope1.psc.00.mgh sysname Linux hostname einstein machine x86_64 user pgautam FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /FREESURFER/lh.thickness.15.mgh logyflag 0 usedti 0 FSGD SA_base.fsgd labelmask /fsaverage/label/lh.cortex.label maskinv 0 glmdir /FREESURFER/lh.pair-thick-T1-00.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /FREESURFER/lh.pair-thick-T1-00.glmdir Loading y from /FREESURFER/lh.thickness.15.mgh INFO: gd2mtx_method is dods Saving design matrix to /FREESURFER/lh.pair-thick-T1-00.glmdir/Xg.dat Normalized matrix condition is 1.30805 Matrix condition is 6.34773 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to /FREESURFER/lh.pair-thick-T1-00.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 DOF = 54 Starting fit and test Matrix is Ill-conditioned 1.000 0.000 1.029 0.000 0.000; 1.000 0.000 0.838 0.000 0.000; 1.000 0.000 0.318 0.000 0.000; 1.000 0.000 0.561 0.000 0.000; 1.000 0.000 0.622 0.000 0.000; 1.000 0.000 0.882 0.000 0.000; 1.000 0.000 2.059 0.000 0.000; 1.000 0.000 0.945 0.000 0.000; 1.000 0.000 1.090 0.000 0.000; 1.000 0.000 1.245 0.000 0.000; 1.000 0.000 0.571 0.000 0.000; 1.000 0.000 0.337 0.000 0.000; 1.000 0.000 1.105 0.000 0.000; 1.000 0.000 0.990 0.000 0.000; 1.000 0.000 1.074 0.000 0.000; 1.000 0.000 1.552 0.000 0.000; 1.000 0.000 1.020 0.000 0.000; 1.000 0.000 0.829 0.000 0.000; 1.000 0.000 0.522 0.000 0.000; 1.000 0.000 1.152 0.000 0.000; 1.000 0.000 0.429 0.000 0.000; 1.000 0.000 1.003 0.000 0.000; 1.000 0.000 0.515 0.000 0.000; 1.000 0.000 1.500 0.000 0.000; 1.000 0.000 -4.639 0.000 0.000; 1.000 0.000 -5.227 0.000 0.000; 1.000 0.000 -5.051 0.000 0.000; 1.000 0.000 -4.918 0.000 0.000; 1.000 0.000 -5.316 0.000 0.000; 1.000 0.000 -5.311 0.000 0.000; 0.000 1.000 0.000 2.172 0.000; 0.000 1.000 0.000 1.115 0.000; 0.000 1.000 0.000 1.056 0.000; 0.000 1.000 0.000 1.372 0.000; 0.000 1.000 0.000 1.267 0.000; 0.000 1.000 0.000 0.847 0.000; 0.000 1.000 0.000 0.682 0.000; 0.000 1.000 0.000 0.524 0.000; 0.000 1.000 0.000 0.682 0.000; 0.000 1.000 0.000 0.930 0.000; 0.000 1.000 0.000 0.126 0.000; 0.000 1.000 0.000 1.113 0.000; 0.000 1.000 0.000 1.066 0.000; 0.000 1.000 0.000 0.517 0.000; 0.000 1.000 0.000 0.598 0.000; 0.000 1.000 0.000 2.061 0.000; 0.000 1.000 0.000 2.003 0.000; 0.000 1.000 0.000 1.204 0.000; 0.000 1.000 0.000 0.975 0.000; 0.000 1.000 0.000 1.445 0.000; 0.000 1.000 0.000 1.327 0.000; 0.000 1.000 0.000 1.731 0.000; 0.000 1.000 0.000 1.610 0.000; 0.000 1.000 0.000 1.145 0.000; 0.000 1.000 0.000 0.102 0.000; 0.000 1.000 0.000 -4.364 0.000; 0.000 1.000 0.000 -5.073 0.000; 0.000 1.000 0.000 -4.607 0.000; 0.000 1.000 0.000 -5.355 0.000; Matrix is Ill-conditioned .. ------------------------------ Message: 8 Date: Thu, 13 Jun 2013 13:21:00 -0400 From: Douglas Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] pvr help To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <51b9ff7c.7020...@nmr.mgh.harvard.edu<mailto:51b9ff7c.7020...@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-1" Hi Prapti, can you send the full terminal output? The ill-conditioned error is probably not related to the contrast. It is usually related to the design matrix, which makes it difficult to track down because you will have a different one at each vertex with --pvr. doug On 6/13/13 1:14 PM, Gautam, Prapti wrote: Dear FreeSurfers I am trying to control for thickness in another surface using the pvr option in mri_glmfit. However, I'm confused as to how I can include the pvr option correctly in the contrast files. I have two groups, and would like to utilize DODS for this analyses as I think that my groups both have different intercepts and slopes. This is my fsgd set up : GroupDescriptorFile1 TitleMyTitle ClassControls CLASS FA VariablesAge InputPMS1Controls14.442163 InputPMS2Controls14.354552 .. InputPMS7FA15.726215 InputPMS28FA14.45859 This is the command I run: mri_glmfit --y lh.surface.mgh --fsgd SA_age.fsgd --C con.mtx --surf fsaverage lh --cortex --glmdir test.glmdir --pvr lh.thickness.psc.mgh --pvr lh.thickness2.psc.mgh The contrast I would like to run is: 0 0 0 0 1 -1 so as to look at group interactions within thickness after controlling for another cortical surface. However, I can't get this to run as there is a "Matrix ill-conditioned" error. The contrast that does run is 0 0 0 0 1 (after passing only one pvr file). But this option seems to be neither dods nor doss. Is there a correct way to do a DODS analyses looking for interactions using the pvr option? Thank you, Prapti --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. 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