INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 6.97972e-07 0.988303

Class Means of each Continuous Variable

1 h_n_f 0.3741

2 h_r_f -0.6420

3 h_n_m -0.8145

4 h_r_m -0.3544

5 b_n_f -0.9296

6 b_r_f -0.7187

7 b_n_m 0.7958

8 b_r_m 0.3549

9 s_n_f 0.4364

10 s_r_f 0.4124

11 s_n_m 0.0769

12 s_r_m -0.6899

INFO: gd2mtx_method is dods

Reading source surface /home/k1895485/scans/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces 327680

Total area 65416.984375

AvgVtxArea 0.399269

AvgVtxDist 0.721953

StdVtxDist 0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /home/k1895485/scans

cmdline mri_glmfit.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir

sysname Linux

hostname login1.nan.kcl.ac.uk

machine x86_64

user k1895485

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y /home/k1895485/scans/lh.g4v1.10.mgh

logyflag 0

usedti 0

FSGD g4v1.fsgd

labelmask /home/k1895485/scans/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.g4v1.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.g4v1.glmdir

Loading y from /home/k1895485/scans/lh.g4v1.10.mgh

... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to lh.g4v1.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 1e+08

Design matrix ------------------

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0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.12483 0.00000 0.00000;

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0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.65852 0.00000 0.00000 0.00000 0.00000 0.00000;

--------------------------------

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.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir

2. The FSGD file (if using one)

3. And the design matrix above

Attempting to diagnose further

SumSq: Min=0.354440 (col 16), Max=2.741043 (col 19)

... could not determine the cause of the problem

Kind Regards,

Marie

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: 03 July 2019 16:22
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec Message to Mailing List

can you send the command line, full terminal output, your fsgd file, and the Xg.dat created in the output?

On 7/3/2019 11:05 AM, Marie Hill wrote:

External Email - Use Caution
Thanks. When I run mri-glmfit I get Error: matrix is ill-conditioned or badly scaled.

I have normalised the continuous variable Age.

Kind regards,

Marie
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: 03 July 2019 15:24
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec Message to Mailing List
yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls mri_glmfit).

On 7/3/2019 9:39 AM, Marie Hill wrote:
External Email - Use Caution

Dear Sir/Madam,

Could I post the following message to the mailing list:

I am running a regression testing for significant difference in cortical volume, thickness etc with 3 factors: diagnosis, genotype and gender, with age as a nuisance factor.

I am using qdec but receiving Error: factor 2 must have 2 levels.

Is it true that Qdec only supports factors with 2 levels? There is a page for qdec levels stating to create a file diagnosis.levels and state the three levels. I did this however the same error occurs.

I was going to use glm_fit instead but I think my study isn't a linear regression so isn't suitable (as I am not interested in the change with age, just between groups).

Kind regards,

Marie
_______________________________________________
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