Dear FreeSurfer experts,

First, I'm very sorry for a newbie question of FreeSurfer.

In my work, there was no problem to analyze a groupwise comparison between controls and patients using QDEC.

However, I've faced a critical problem to acquire a statistical result from the comparison between a control group(n=23) and an individual patient as follows:

I got success to analyze the statistical comparison without any continuous(covariate) or Nuisance factors.

The error is only ocurred when I selected one of continous or nuisance factors.

I failed to search the proper post to resolve my problem via FreeSurfer Achieve.

Please would you give me a solution for it?

I also attached the log file for my error.

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Loading data table /home/gitamen/Study/FCD_Study_2nd_edit/qdec/NMLvsIndividual.dat...

Number of columns: 4

fsid column: 1

Number of factors: 3

Number of subjects: 24

Data table /home/gitamen/Study/FCD_Study_2nd_edit/qdec/NMLvsIndividual.dat loaded.

Verifying subject data........................Subject verification complete.

Input table: /home/gitamen/Study/FCD_Study_2nd_edit/qdec/NMLvsIndividual.dat

Subj#, SubjID, Data...

1 NML001 NML 39.000000 1.166685

2 NML002 NML 45.000000 1.241351

3 NML003 NML 39.000000 1.097524

4 NML004 NML 41.000000 1.266187

5 NML005 NML 38.000000 1.241621

6 NML007 NML 34.000000 1.286933

7 NML008 NML 38.000000 1.115885

8 NML009 NML 37.000000 1.252660

9 NML010 NML 32.000000 1.162417

10 NML012 NML 57.000000 1.105987

11 NML013 NML 46.000000 1.084537

12 NML014 NML 28.000000 1.055648

13 NML017 NML 46.000000 1.199341

14 NML018 NML 35.000000 1.001247

15 NML021 NML 52.000000 1.296659

16 NML022 NML 43.000000 1.316231

17 NML023 NML 40.000000 1.260854

18 NML024 NML 55.000000 1.149161

19 NML025 NML 52.000000 1.072912

20 NML026 NML 52.000000 1.295002

21 NML028 NML 35.000000 1.099504

22 NML029 NML 43.000000 0.969897

23 NML030 NML 55.000000 1.228311

24 T1003 FCD 42.000000 1.198920

1 Group discrete 2

1 NML

2 FCD

2 Age continuous 0

3 eTIV continuous 0

Continuous Factors: Mean: StdDev:

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

Age 42.667 7.894

eTIV 1.174 0.098

Number of subjects: 24

Number of factors: 3 (1 discrete, 2 continuous)

Number of classes: 2

Number of regressors: 6

============================================================

Data table loading completed successfully.

SUBJECTS_DIR is '/home/gitamen/Study/FCD_Study_2nd_edit'

lh-Avg-Intercept-thickness -----------------------

Does the average thickness differ from zero?

Nuisance factors: eTIV

1.000 1.000 0.000 0.000;

lh-Diff-NML-FCD-Intercept-thickness -----------------------

Does the average thickness differ between NML and FCD?

Nuisance factors: eTIV

1.000 -1.000 0.000 0.000;

ninputs = 24

Checking inputs

nframestot = 24

Allocing output

Done allocing

nframes = 24

Writing to /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/y.mgh

gdfReadHeader: reading /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/qdec.fsgd

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

Continuous Variable Means (all subjects)

0 eTIV 1.17356 0.0962103

Class Means of each Continuous Variable

1 GroupNML 1.1725

2 GroupFCD 1.1989

INFO: gd2mtx_method is dods

Reading source surface /home/gitamen/Study/FCD_Study_2nd_edit/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 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /home/gitamen/Study/FCD_Study_2nd_edit/qdec

cmdline mri_glmfit --y /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/y.mgh --fsgd /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/qdec.fsgd dods --glmdir /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT --surf fsaverage lh --label /home/gitamen/Study/FCD_Study_2nd_edit/fsaverage/label/lh.aparc.label --C /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/contrasts/lh-Avg-Intercept-thickness.mat --C /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/contrasts/lh-Diff-NML-FCD-Intercept-thickness.mat

sysname Linux

hostname u203.gpu74.samsung.co.kr

machine x86_64

user gitamen

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/y.mgh

logyflag 0

usedti 0

FSGD /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/qdec.fsgd

labelmask /home/gitamen/Study/FCD_Study_2nd_edit/fsaverage/label/lh.aparc.label

maskinv 0

glmdir /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT

Loading y from /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/y.mgh

INFO: gd2mtx_method is dods

Saving design matrix to /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/Xg.dat

Normalized matrix condition is 1e+08

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

1.000 0.000 1.167 0.000;

1.000 0.000 1.241 0.000;

1.000 0.000 1.098 0.000;

1.000 0.000 1.266 0.000;

1.000 0.000 1.242 0.000;

1.000 0.000 1.287 0.000;

1.000 0.000 1.116 0.000;

1.000 0.000 1.253 0.000;

1.000 0.000 1.162 0.000;

1.000 0.000 1.106 0.000;

1.000 0.000 1.085 0.000;

1.000 0.000 1.056 0.000;

1.000 0.000 1.199 0.000;

1.000 0.000 1.001 0.000;

1.000 0.000 1.297 0.000;

1.000 0.000 1.316 0.000;

1.000 0.000 1.261 0.000;

1.000 0.000 1.149 0.000;

1.000 0.000 1.073 0.000;

1.000 0.000 1.295 0.000;

1.000 0.000 1.100 0.000;

1.000 0.000 0.970 0.000;

1.000 0.000 1.228 0.000;

0.000 1.000 0.000 1.199;

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

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 --y /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/y.mgh --fsgd /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/qdec.fsgd dods --glmdir /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT --surf fsaverage lh --label /home/gitamen/Study/FCD_Study_2nd_edit/fsaverage/label/lh.aparc.label --C /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/contrasts/lh-Avg-Intercept-thickness.mat --C /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/contrasts/lh-Diff-NML-FCD-Intercept-thickness.mat

2. The FSGD file (if using one)

3. And the design matrix above

Error in Analyze: command failed: mri_glmfit --y /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/y.mgh --fsgd /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/qdec.fsgd dods --glmdir /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT --surf fsaverage lh --label /home/gitamen/Study/FCD_Study_2nd_edit/fsaverage/label/lh.aparc.label --C /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/contrasts/lh-Avg-Intercept-thickness.mat --C /home/gitamen/Study/FCD_Study_2nd_edit/qdec/TTT/contrasts/lh-Diff-NML-FCD-Intercept-thickness.mat