External Email - Use Caution
Hi profesor Greve,
I believe I have located the problem, as you will see in the code below it
seems one of the groups (FemalePDMCI) has only 7 subjects and (MALEPDMCI) has
13 which means the regression won't have enough DOF. They amount of DOF needed
is NregressorsDODS = Nclasses*(Nvariables+1) = 4*(4+1) =
20. Therefore I believe I would have to renounce to divide my subjects in Males
and Females. Here is the output, let me know if that was the main issue.
Thanks.
Vicente,
mri_glmfit --y $PRJDIR/FREESURFER_PPMI/stats/$image.nii.gz \
> --fsgd $PRJDIR/FREESURFER_PPMI/stats/glm_covariates_moca_groups.fsgd dods \
> --C $PRJDIR/FREESURFER_PPMI/stats/contrast_moca_groups.mtx \
> --glmdir $PRJDIR/FREESURFER_PPMI/stats/$image.corr_g_glmdir --eres-save
> --illcond
gdfRead(): reading
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/glm_covariates_moca_groups.fsgd
mri_glmfit-sim --glmdir $PRJDIR/FREESURFER_PPMI/stats/$image.corr_g_glmdir \
--cwp .9 \
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 age 0.00273866 1.00533
1 relative_motion 0.0142075 0.995938
2 dis_duration 0.00767562 1.0031
3 moca 0.0168011 0.991508
Class Size and Means of each Continuous Variable
1 MaleHC 35 0.0125 0.2192 -0.6716 0.1872
2 MalePDCN 63 0.0523 -0.0415 0.2829 0.2509
3 MalePDMCI 13 0.4036 0.4899 0.1774 -2.0122
4 FemaleHC 20 -0.2146 -0.0406 -0.6716 0.1562
5 FemalePDCN 37 -0.1703 -0.1990 0.4623 0.4639
6 FemalePDMCI 7 0.2990 -0.1089 0.1496 -1.9348
INFO: gd2mtx_method is dods
7.3.2
cwd /export/home/vferrer
cmdline mri_glmfit --y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.nii.gz
--fsgd
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/glm_covariates_moca_groups.fsgd
dods --C
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/contrast_moca_groups.mtx
--glmdir
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir
--eres-save --illcond
sysname Linux
hostname ipsnode-7-3.local
machine x86_64
user vferrer
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.nii.gz
logyflag 0
usedti 0
FSGD
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/glm_covariates_moca_groups.fsgd
glmdir
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir
IllCondOK 1
ReScaleX 1
DoFFx 0
Creating output directory
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir
--perm 1000 1.5 abs --overwrite --perm-force --seed 1669778971
Loading y from
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.nii.gz
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Matrix condition is 3.69944e+08
Pruning voxels by thr: 1.175494e-38
Found 47 voxels in mask
Saving mask to
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh
search space = 158.625000
DOF = 145
Starting fit and test
Fit completed in 0.000783333 minutes
Computing spatial AR1 in volume.
fMRIspatialAR1(): hit 0 voxels
WARNING: no voxels in AR1 computation
Residual: ar1mn = (-nan,-nan,-nan) fwhm = (-nan,-nan,-nan) -nan
Writing results
contrast_moca_groups
maxvox sig=0.000253964 F=5.38727e-07 at index 42 0 0 seed=1670287315
Computing efficiency
mri_glmfit done
[vferrer@ipsnode-7-3 ~]$
[vferrer@ipsnode-7-3 ~]$ mri_glmfit-sim --glmdir
$PRJDIR/FREESURFER_PPMI/stats/$image.corr_g_glmdir \
> --cwp .9 \
> --perm 1000 1.5 abs --overwrite --perm-force --seed 1669778971
cmdline mri_glmfit --y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.nii.gz
--fsgd
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/glm_covariates_moca_groups.fsgd
dods --C
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/contrast_moca_groups.mtx
--glmdir
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir
--eres-save --illcond
mri_info --dim
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh
--o /scratch/vferrer/tmp.suxi2S
Turning on 1D dim = 47 1 1 1
log file is
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/perm.th15.abs.mri_glmfit-sim.log
cd /export/home/vferrer
/opt/freesurfer-7.3.2/bin/mri_glmfit-sim
--glmdir
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir
--cwp .9 --perm 1000 1.5 abs --overwrite --perm-force --seed 1669778971
mri_glmfit-sim 7.3.2
Tue Nov 29 16:06:54 CET 2022
Linux ipsnode-7-3.local 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
vferrer
setenv SUBJECTS_DIR /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI
FREESURFER_HOME /opt/freesurfer-7.3.2
Original mri_glmfit command line:
cmdline mri_glmfit --y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.nii.gz
--fsgd
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/glm_covariates_moca_groups.fsgd
dods --C
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/contrast_moca_groups.mtx
--glmdir
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir
--eres-save --illcond
DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
Seed = 1669778971
fwhm = 0
nSimPerJob = 1000
1/1 Tue Nov 29 16:06:54 CET 2022
mri_glmfit --C
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-21231/contrast_moca_groups.mtx
--sim perm 1000 1.5
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001
--sim-sign abs --fwhm 0 --fsgd
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
dods --mask
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh
--y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
--perm-force --seed 1669778971
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
simbase
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001
FWHM = 0.000000
gdfRead(): reading
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 age 0.00273894 1.00533
1 relative_motion 0.0142074 0.995939
2 dis_duration 0.0076754 1.0031
3 moca 0.0168018 0.991509
Class Size and Means of each Continuous Variable
1 MaleHC 35 0.0125 0.2192 -0.6716 0.1872
2 MalePDCN 63 0.0523 -0.0415 0.2829 0.2509
3 MalePDMCI 13 0.4037 0.4899 0.1774 -2.0122
4 FemaleHC 20 -0.2146 -0.0406 -0.6716 0.1562
5 FemalePDCN 37 -0.1703 -0.1990 0.4623 0.4639
6 FemalePDMCI 7 0.2990 -0.1089 0.1496 -1.9348
INFO: gd2mtx_method is dods
7.3.2
cwd /export/home/vferrer
cmdline mri_glmfit --C
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-21231/contrast_moca_groups.mtx
--sim perm 1000 1.5
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001
--sim-sign abs --fwhm 0 --fsgd
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
dods --mask
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh
--y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
--perm-force --seed 1669778971
sysname Linux
hostname ipsnode-7-3.local
machine x86_64
user vferrer
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
logyflag 0
usedti 0
FSGD
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
mask
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
... done reading.
INFO: gd2mtx_method is dods
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix ------------------
--------------------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
--------------------------------
-------- ERROR: READ THIS -----------------
--vvvvvvvvvvvvvvvvvvvvvvvvvvvvvv-----
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 --C
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-21231/contrast_moca_groups.mtx
--sim perm 1000 1.5
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001
--sim-sign abs --fwhm 0 --fsgd
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
dods --mask
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh
--y
/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
--perm-force --seed 1669778971
2. The terminal output of this program (ie, everything it prints to the
screen)
3. The FSGD file
(/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd)
4. The design matrix (null)/Xg.dat
Attempting to diagnose further
SumSq: Min=1.455099 (col 24), Max=8.657582 (col 23)
... could not determine the cause of the problem
--^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^----
Vicente Ferrer
Predoctoral Researcher BCBL
http://secure-web.cisco.com/1Dnpd94Rs0IQlR6VloIhAgiyFb_RpyRiiy3jpkQjDeBYo20evwIMEwITcF1H9T--PJPJsZPeYZoLed6ACMrT7GC-CubowSFeRnaVSRQSrRBGCX0QEcP4a5QZDbzB7ZMChOJTZSHSJyX8fQLdAxmGOxt4Vq9h28sx1D7ZNEO9BHFGicJaBlHgB5IYrLzKjWrkuO8Xc8uPsrap7mND0OJqEAePJ3tznONbbjjAmU70BLNm-Ag9RQNX2lEgi8VePrwkXsIPdLfaeVI33azDgT_hcRB87UzHAQ9fqqYjB_yV4umMV1YcjD_tv375GQA4fkAyZ/http%3A%2F%2Fwww.bcbl.eu
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----- Original Message -----
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, November 28, 2022 3:04:50 AM
Subject: Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled,
condno = 1e+08
that is quite strange. Does it happen every time? What is the
mri_glmfit-sim command line and terminal output?
On 11/23/2022 2:47 PM, Vicente Ferrer wrote:
> External Email - Use Caution
>
> Dear Freesurfer users,
>
> I was trying yo use mri_glmfit-sim after using mri_glmfit that run
> successfully and I encounter this error:
>
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>
>
> --------------------------------
> -------- ERROR: READ THIS -----------------
> --vvvvvvvvvvvvvvvvvvvvvvvvvvvvvv-----
> 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 --C
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-29440/contrast_moca_groups.mtx
> --sim perm 1000 1.5
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_b
> br.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001 --sim-sign abs --fwhm 0 --fsgd
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd
> dods --mask /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg
> 16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh --y
> /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh
> --perm-force --seed 1669778971
> 2. The terminal output of this program (ie, everything it prints to the
> screen)
> 3. The FSGD file
> (/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd)
> 4. The design matrix (null)/Xg.dat
> Attempting to diagnose further
> SumSq: Min=1.455099 (col 24), Max=8.657582 (col 23)
> ... could not determine the cause of the problem
> --^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^----
>
> Seems like there is a problem with the condition matrix, but I do not
> understand why. Could you help me with this problem? I attached the contrast
> and fsgd files
>
> Best,
> Vicente Ferrer
> Predoctoral Researcher BCBL
> https://secure-web.cisco.com/1LltUaRD73SETA6gdKJYUJ2TOvuENOJaNZO4-8mWNgOMdlQCoa_sUW_ZQTf95PUj8t6eYzLPTzgRh1_09ymiZA67iF7bs9VDsOjp1dPJHoJzziqEUobtfHm1Psm5QwPOXVnpmU8o6gSgXQnAbtE_6yQUfqoU_g5FGM8vtxf5Lz-WNZfUcBhWcz5-MaJpKe3yw7Hiv765avkYx6nTYAbrvcEBN7E1kMUKXM5MVlpjMB-db8O-xisYr1dJTTiikY1Ej8xYt6EDxJi-8ZvyY7Uv4K4lnSdvvZCrNXh81GdRup8H2fVad3e8VUFfPNh0VJ97Z/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsecure-web.cisco.com%2F1kWZEOu8GTFhJvEwUHVoEpHYRwVtjwPjaW-68jFXGIsKvsccvtZ_SpRT4mbfMn9yTEj2SS5sODMuPyTAI7wxqhCmRxBRJ-35S_I8dxkyBkn-mSO5ejNKj3y_fRHlzfZYF0Y7e4avfl65oYvF1P9f6zlpO9fvp61CMx3UMDUkUt33HANwhKrNAQrsy2Y5VCcoRrA2AKBS0Z5P-jUa88tp7dylA1Zd2jmD5f7dpneDGC1UTgcKCSiQESkTtkx8M29TK78bxICiS2DYkMxYTENKlkex0JPgoayYX8JXmUgwvPcKnzKLxI-NITvFv7ql7vHrpEha80-krYMT5O5ictU2HZA%2Fhttp*3A*2F*2Fwww.bcbl.eu__;JSUl!!D9dNQwwGXtA!TjwEwxlcphP94Eem0VV_Ac5cyRfTuBgB2oEHsWsri2po-UDTIxqY3ZvzNfn5hDA4gGsn1MkRFVGg6njUUPa9Iw$
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