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Hi experts,

I am running following command:

mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

Both FSGD and Contrast files are also attached.

After I run above command, I get following error (highlighted in red):

mri_glmfit --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

gdfRead(): reading PAI_SUI_ONLY_MILD_DEP2.fsgd

INFO: demeaning continuous variables

Continuous Variable Means (all subjects)

0 SUI 52.4444 2.11403

1 Age 32.1111 7.23332

2 DEP 55.1111 7.83786

Class Means of each Continuous Variable

1 Male 52.0000 32.0000 54.0000

2 Female 52.6667 32.1667 55.6667

INFO: gd2mtx_method is dods

Reading source surface /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/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 /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral

cmdline mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

sysname Linux

hostname hyperion

machine x86_64

user scanlab

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh

logyflag 0

usedti 0

FSGD PAI_SUI_ONLY_MILD_DEP2.fsgd

labelmask /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/label/lh.cortex.label

maskinv 0

glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

Loading y from /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh

... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 1e+08

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

0.00000 1.00000 0.00000 1.68188 0.00000 -0.01536 0.00000 -1.67279;

1.00000 0.00000 -0.68326 0.00000 1.09063 0.00000 -0.77969 0.00000;

0.00000 1.00000 0.00000 -0.68326 0.00000 -1.39785 0.00000 2.02720;

0.00000 1.00000 0.00000 -0.68326 0.00000 1.22888 0.00000 -0.14176;

1.00000 0.00000 0.73582 0.00000 -0.29186 0.00000 0.62375 0.00000;

1.00000 0.00000 -0.68326 0.00000 -0.84486 0.00000 -0.26935 0.00000;

0.00000 1.00000 0.00000 1.68188 0.00000 -1.12135 0.00000 0.11341;

0.00000 1.00000 0.00000 -0.68326 0.00000 1.50538 0.00000 -0.65211;

0.00000 1.00000 0.00000 -0.68326 0.00000 -0.15361 0.00000 0.75134;

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

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 SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

2. The FSGD file (if using one)

3. And the design matrix above

Attempting to diagnose further

SumSq: Min=1.034183 (col 7), Max=2.816108 (col 8)

... could not determine the cause of the problem

Both fsgd and contrast files are created in LINUX, and I also normalized my data using DeMeanFlag 1

ReScaleFlag 1 as suggested here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49123.html

Could you please help in resolving this issue?

Thanks !

Sahil