Hi Freesurfer Experts, I am trying to run mri_glmfit and while 90% of my files work, some of them display the error below. I have tried demeaning, and then tried multiplying this value by 100, and I still get the same error. Any feedback would be greatly appreciated.
mris_preproc done
srcsubject = fsaverage
srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
srctype =
trgsubject = fsaverage
trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
trgtype =
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi = rh
trghemi = rh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = (null)
label-trg = (null)
OKToRevFaceOrder = 1
Reading source surface reg
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
Loading source data
INFO: trgsubject = srcsubject
Saving target data
Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
gdfReadHeader: reading
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 19.5833 1.32025
1 eTIV 1.61645e+06 145343
2 EnglishParityRT 0.00012207 25139.1
Class Means of each Continuous Variable
1 Monolingual_male 19.7143 1678946.5893 -4197.2796
2 Monolingual_female 19.4000 1528966.6750 5876.1917
INFO: gd2mtx_method is dods
Reading source surface
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /gpfs/scratch/jtl190/Math_reconstruction
cmdline mri_glmfit --y
rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
--C
/gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
--surf fsaverage rh --cortex --glmdir
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
sysname Linux
hostname cyberstar129.hpc.rcc.psu.edu
machine x86_64
user jtl190
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
logyflag 0
usedti 0
FSGD
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
labelmask
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
Loading y from
/gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
Normalized matrix condition is 22568.9
Design matrix ------------------
1.000 0.000 18.000 0.000 1865790.250 0.000 -8952.208 0.000;
0.000 1.000 0.000 19.000 0.000 1520429.625 0.000 -4605.208;
1.000 0.000 19.000 0.000 1749716.750 0.000 -39407.207 0.000;
0.000 1.000 0.000 18.000 0.000 1589109.250 0.000 -17967.209;
1.000 0.000 21.000 0.000 1472295.125 0.000 19531.791 0.000;
1.000 0.000 18.000 0.000 1580381.375 0.000 -17027.209 0.000;
1.000 0.000 20.000 0.000 1813373.500 0.000 16152.792 0.000;
1.000 0.000 21.000 0.000 1638616.500 0.000 -9074.208 0.000;
0.000 1.000 0.000 21.000 0.000 1297920.500 0.000 61860.793;
0.000 1.000 0.000 18.000 0.000 1634762.625 0.000 -22671.209;
0.000 1.000 0.000 21.000 0.000 1602611.375 0.000 12763.792;
1.000 0.000 21.000 0.000 1632452.625 0.000 9395.292 0.000;
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9
--------------------------------
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 rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
--fsgd
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
--C
/gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
--surf fsaverage rh --cortex --glmdir
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
2. The FSGD file (if using one)
3. And the design matrix above
I am also attaching the FSGD file.
Best,
Jennifer Legault
fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
Description: Binary data
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