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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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.
_______________________________________________
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.