Can you email the fsgd file?
On 5/12/2020 1:35 PM, Marina Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
I get the error that you can find at the end of this message when I am
running mri_glmfit.
Whenever I run an analysis in which the experimental design has more
than 12 columns, I get the same error, whereas if the experimental
design has less than 12 columns, the analysis is successful.
I also send you the fsgd.txt file (through FTP File Exchange). In this
file you can see that there are four groups that have been created by
the combination of two discrete variables (sex and apoe-type).
How can I solve this problem?
Thank you in advance.
ERROR MESSAGE:
(...)
Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix ------------------
0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000
0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.79984
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000
0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.84287
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.74935 0.00000
0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.82284
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000 0.00000
0.00000 -0.32012 0.00000 0.00000 0.00000 0.17882 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000
0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.33908
0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.71704
0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000
-0.02652 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.66002 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000
0.00000 0.46929;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.48385 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000
0.00000 1.23055;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.83619 0.00000 0.00000 0.00000 -2.38637 0.00000 0.00000
0.00000 -0.90297;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000
0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.28399
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000
0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.86996
0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
1.18853 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000
0.00000 0.18883;
0.00000 1.00000 0.00000 0.00000 0.00000 -2.15871 0.00000
0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 1.53105
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -1.98254 0.00000 0.00000
0.00000 0.50638 0.00000 0.00000 0.00000 0.73974 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000
0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.23391
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 0.13151 0.00000
0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.91298
0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
-1.63020 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000
0.00000 0.78982;
0.00000 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000
0.00000 0.00000 -1.55987 0.00000 0.00000 0.00000 -0.15173
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 1.54087 0.00000 0.00000
0.00000 -0.32012 0.00000 0.00000 0.00000 1.28564 0.00000
0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.30768
0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000
-0.76775 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
1.71704 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000
0.00000 1.41085;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.48385 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000
0.00000 0.73974;
1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000
0.00000 1.53950 0.00000 0.00000 0.00000 -0.76274 0.00000
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 0.66002 0.00000 0.00000
0.00000 0.91963 0.00000 0.00000 0.00000 -0.50731 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000
0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 -0.93803
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000
0.00000 0.29975 0.00000 0.00000 0.00000 -1.07325 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000
0.00000 0.00000 1.74613 0.00000 0.00000 0.00000 -0.46725
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000
0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -1.50396
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000
0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.65460
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -1.10169 0.00000
0.00000 0.00000 1.12625 0.00000 0.00000 0.00000 -0.26191
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000
0.00000 0.00000 1.53950 0.00000 0.00000 0.00000 0.05361
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000
0.00000 0.00000 0.71300 0.00000 0.00000 0.00000 -0.77776
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -0.22083 0.00000 0.00000
0.00000 -0.32012 0.00000 0.00000 0.00000 0.94007 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.74935 0.00000
0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 0.76979
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.71704 0.00000
0.00000 0.00000 -1.76650 0.00000 0.00000 0.00000 -3.43214
0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.30768 0.00000 0.00000 0.00000 -0.94000 0.00000 0.00000
0.00000 0.60452;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
-0.92552 0.00000 0.00000 0.00000 -0.11350 0.00000 0.00000
0.00000 0.61954;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
-0.22083 0.00000 0.00000 0.00000 0.50638 0.00000 0.00000
0.00000 0.91503;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000
0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 -0.16175
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -1.27786 0.00000
0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 0.80485
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000
0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.21888
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000
0.00000 1.53950 0.00000 0.00000 0.00000 -0.28194 0.00000
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -0.22083 0.00000 0.00000
0.00000 -0.52675 0.00000 0.00000 0.00000 -0.49229 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -1.98254 0.00000
0.00000 0.00000 0.71300 0.00000 0.00000 0.00000 0.69968
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000
0.00000 0.00000 -0.11350 0.00000 0.00000 0.00000 -0.71766
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000 0.00000
0.00000 0.91963 0.00000 0.00000 0.00000 -0.55239 0.00000
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -1.10169 0.00000 0.00000
0.00000 -0.11350 0.00000 0.00000 0.00000 -2.14502 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000
0.00000 0.00000 -0.94000 0.00000 0.00000 0.00000 -1.17341
0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.48385 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000
0.00000 2.19214;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.92552 0.00000
0.00000 0.00000 0.71300 0.00000 0.00000 0.00000 -1.38877
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000
0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.08662
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.36470 0.00000
0.00000 0.00000 -1.35325 0.00000 0.00000 0.00000 0.66462
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.36470 0.00000
0.00000 0.00000 1.12625 0.00000 0.00000 0.00000 0.71971
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.18853 0.00000
0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 0.58448
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -1.63020 0.00000
0.00000 0.00000 0.50638 0.00000 0.00000 0.00000 0.95009
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000
0.00000 0.00000 -1.97312 0.00000 0.00000 0.00000 -0.47226
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000
0.00000 0.00000 -1.14662 0.00000 0.00000 0.00000 -0.45222
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 1.18853 0.00000 0.00000
0.00000 -0.11350 0.00000 0.00000 0.00000 0.12372 0.00000
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000
0.00000 -1.35325 0.00000 0.00000 0.00000 -0.26191 0.00000
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.18853 0.00000
0.00000 0.00000 -1.35325 0.00000 0.00000 0.00000 -0.12168
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000
0.00000 0.00000 1.53950 0.00000 0.00000 0.00000 0.39417
0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
-1.45403 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000
0.00000 -0.53737;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
0.30768 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000
0.00000 1.10534;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
1.01236 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000
0.00000 0.46429;
0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000
0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.33908
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000
0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 0.32906
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000
0.00000 -1.55987 0.00000 0.00000 0.00000 -1.73434 0.00000
0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000
1.01236 0.00000 0.00000 0.00000 1.12625 0.00000 0.00000
0.00000 1.63622;
0.00000 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000
0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.98310
0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000
0.00000 0.00000 2.36600 0.00000 0.00000 0.00000 -2.40545
0.00000 0.00000;
1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000 0.00000
0.00000 -0.52675 0.00000 0.00000 0.00000 1.24557 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 --surf amy_frapsaliva_average lh --C
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/contrast.mat
--fsgd /usr/local/freesurfer/subjects/amy_frapsaliva_stats/fsgd.txt
dods --label
/usr/local/freesurfer/subjects/amy_frapsaliva_average/label/lh.cortex.label
--y
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/lh.fsgd_subj_gauss001.mgh
--no-prune --glmdir
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001
2. The FSGD file (if using one)
3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.768203 (col 15), Max=6.706254 (col 10)
... could not determine the cause of the problem
_______________________________________________
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
