Hello again,
I also tried the command line options. I get an error for ill-conditioned matrix. Could it be because of possible correlations between covariates? For example I am using Age and mean thickness, should I just use one of them?
Here is the error:
wrls-guest-166-198:subjects manishdalwani$ mri_glmfit --y lh.thickness.CD.10.mlh.thickness.CD.10.mgh lh.thickness.CD.10.mris_preproc.log wrls-guest-166-198:subjects manishdalwani$ mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir gdfReadHeader: reading FSGD_CD.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 16.6492 1.13124 1 Meanthickness 2.4772 0.0616129 2 IQ 98.08 8.24097 3 CD 6.44 2.77244 Class Means of each Continuous Variable 1 PATIENTS 16.6492 2.4772 98.0800 6.4400 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir sysname Darwin hostname wrls-guest-166-198.ucdenver.edu machine i386 user manishdalwani FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.thickness.CD.10.mgh logyflag 0 usedti 0 FSGD FSGD_CD.fsgd labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness_CD.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness_CD.glmdir Loading y from /Applications/freesurfer/subjects/lh.thickness.CD.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.thickness_CD.glmdir/Xg.dat Normalized matrix condition is 22815.1 Design matrix ------------------ 1.000 15.320 2.500 104.000 2.000; 1.000 18.250 2.440 113.000 9.000; 1.000 18.080 2.460 108.000 3.000; 1.000 14.600 2.560 96.000 11.000; 1.000 14.350 2.580 109.000 6.000; 1.000 17.620 2.530 90.000 6.000; 1.000 16.990 2.500 102.000 7.000; 1.000 17.720 2.450 96.000 6.000; 1.000 17.170 2.450 99.000 7.000; 1.000 17.100 2.360 92.000 1.000; 1.000 16.010 2.460 83.000 4.000; 1.000 17.040 2.430 95.000 4.000; 1.000 17.730 2.490 104.000 2.000; 1.000 15.280 2.480 100.000 8.000; 1.000 16.440 2.390 105.000 10.000; 1.000 16.700 2.580 95.000 8.000; 1.000 16.840 2.460 93.000 9.000; 1.000 17.710 2.380 115.000 5.000; 1.000 15.120 2.470 86.000 11.000; 1.000 16.780 2.520 99.000 7.000; 1.000 15.100 2.420 86.000 5.000; 1.000 16.060 2.510 88.000 6.000; 1.000 18.490 2.430 92.000 7.000; 1.000 16.700 2.610 102.000 11.000; 1.000 17.030 2.470 100.000 6.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 22815.1 -------------------------------- 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 lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir 2. The FSGD file (if using one) 3. And the design matrix above
________________________________ From: Manish Dalwani manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Monday, June 24, 2013 1:01 PM Subject: Re: [Freesurfer] Help with QDEC error
Hi Nick and Doug,
Can you suggest an alternative way if QDEC is unable to handle a single group? I would like to run these analyses to address reviewers comments.
Best, Manish
________________________________ From: Douglas Greve greve@nmr.mgh.harvard.edu To: Manish Dalwani manishdalwani@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 20, 2013 11:16 PM Subject: Re: [Freesurfer] Help with QDEC error
I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug
On 6/20/13 12:36 PM, Manish Dalwani wrote:
Hi Doug and Freesurfers,
I realized that I hadn't updated my group levels to one group. However, when I do that..the qdec complains about group.level having at minimum two levels. How can I run (using QDEC) single group regression?
Thanks, Manish
From: Manish Dalwani manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 20, 2013 1:26 PM Subject: Re: [Freesurfer] Help with QDEC error
Hi Doug,
I was out of town for a conference. Please see my attachments. I have the log file and screenshots of ill-matrix conditioning. Thanks for your help! Manish
From: Douglas Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Saturday, June 15, 2013 11:09 AM Subject: Re: [Freesurfer] Help with QDEC error
Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug
On 6/14/13 4:57 PM, Manish Dalwani wrote:
Hello Freesurfers,
I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error:
Qdec 1.4 (Qdec1.4)
Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C
/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat
Please advice!
Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado
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