External Email - Use Caution Hello Freesurfer experts,
I am trying to perform a GLM, using the volume of a brain region as a covariate. I am doing a two-group, one covariate design. I originally tried to use QDEC to facilitate the process and received an error message that the mri_glmfit command had failed. I then saw that QDEC was deprecated and followed the instructions set out on the freesurfer wiki for doing it manually (https://secure-web.cisco.com/1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGWz8ZAzr0ToHAdQVWw6seyPj2yu31w7pqzGFZrFu7wQ5so3ZFfYQjKCTQ_ExMc1qL3caPs38GvVhvpKQ2NXDmLYaNxgZkGAilAmdd8JnWqAEkh_EBy23scDzimQ4p5fuMO002JYf6Si2hgy5xDHl5Yf748DEHIe1u3vA-E3BtAxiCGBB67Hm4Dc6xHuUk_Na_DLM_uYMDcy3z8UttfwM1TTMP0_JLn_rmvpcqSqGN2rtaA3UGOE5aOOm0GnQgDXQWm5MIgG9_A0PeUuBfAxRgunRr7ZxcVBapNEIOwCUPdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0). I received the same error message as I had with QDEC on the command line: ERROR: MatrixResidualForming(): X is not invertable RD is not invertable n = 1 This only occurs for certain of the brain regions used as covariates; for others, the QDEC and command-line streams work perfectly. Additionally, I've noticed that if I input different numbers for the covariate values in the fsgd file, the command runs smoothly. I haven't been able to find a similar error on the mailing list, does anyone have an idea of how to work around this? I would greatly appreciate it. Please find attached my fsgd file, and the full log of what happens after I run the mri_glmfit command (when it works and when it doesn't) The hands.fsgd file doesn't work, whereas the hands_works.fsgd file does. Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL Best wishes, Alex -- Alexandre Piot, MSc. Queen Square Institute of Neurology President of the Application of Psychedelics Society <https://secure-web.cisco.com/1txv4iCOx4-mObxXkQBwlHnKAPMdNbmkUOMySvRIxTq9ls1uXZ8Kl62y3I49HdkLsX6y7u-cbb0hhFAgyYtQiLyvLqmJHRpVile95hsJIW_BkEPsZYU7xlCSImzrBqWQ04vGC-z5o197phurtwnpjWg9swrt2VVrxiiXYGg9bY0RbMOrknb9AaoPwF5FSDuMc0WVXrwnhjXQY6v4i38hVb6sLx6MLR2rCdDLI8W_lEtTFtoddcERVMfMlp1QPST7zgdW1ISSG1NIw0Y7AGPrRMAOgyDEDDbcO5Bw5ZAdy0JZpVjRnYzg9UIT_Svi--kUWS1MEmI_sDO3lstJ-3GIgMQ/https%3A%2F%2Fwww.uclsap.com%2F> -- UCL UNITy Project<https://secure-web.cisco.com/11-VCBFrldtskQk64mTlGciM29YjbhiPBFq0qJNEn4t16fq2dpqPk8MULNrPk_hdW3xFgDWoez2dpX7V5EsWwjhjv5xLowcqQlWm8H8z1bfrLct3k0RqTnpX1n8ctYdYTBN4YZweUcivxmxcuvMem-Gc6V7-VqRYMBpF6H6kHTK_UcUi5UnP5yWRqhIkMLWkdPffFie-WcMxkLkdKIpTISAHztKFwrtv1Z0KJlrr03qryskIQu6LNxCa5spVh0LxIs6qkUPD7pRD2E8dl-jERSFNiw0WJygtI9HdMjxfWc8x9C2KVtbdX5UmF1A-hcqoRaqNXrfS42WsaQI_sTTEKdA/https%3A%2F%2Fwww.psychedelicunit.com%2F>
mri_glmfit.log
Description: mri_glmfit.log
hand.fsgd
Description: hand.fsgd
mri_glmfit --y
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
--fsgd
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
--glmdir
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
--surf fsaverage lh --label
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-volume-lh_cingul-ant_volume-Cor.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Cor-volume-lh_cingul-ant_volume.mat
gdfRead(): reading
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 lh_G_frontomargin_volume 2404.2 361.981
Class Size and Means of each Continuous Variable
1 GroupAyahuasca 22 2355.0909
2 GroupControl 22 2453.3182
INFO: gd2mtx_method is dods
Reading source surface
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65417.000000
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195472
7.2.0
cwd
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
cmdline mri_glmfit --y
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
--fsgd
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
--glmdir
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
--surf fsaverage lh --label
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-volume-lh_cingul-ant_volume-Cor.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Cor-volume-lh_cingul-ant_volume.mat
sysname Linux
hostname Zenbook
machine x86_64
user psychedelic
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
logyflag 0
usedti 0
FSGD
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
labelmask
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
maskinv 0
glmdir
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
Loading y from
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/Xg.dat
Computing normalized matrix
Normalized matrix condition is 209.313
Matrix condition is 3.24526e+08
Found 148151 points in label.
Pruning voxels by thr: 1.175494e-38
Found 146665 voxels in mask
Saving mask to
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/mask.mgh
Reshaping mriglm->mask...
search space = 72932.786449
DOF = 40
Starting fit and test
Fit completed in 0.04985 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995918, ar1std=0.002169, gstd=6.327300, fwhm=14.899653
Writing results
lh-Avg-Intercept-volume
maxvox sig=11.5306 F=97.0993 at index 154924 0 0 seed=1662639010
lh-Avg-volume-lh_cingul-ant_volume-Cor
maxvox sig=14.4629 F=151.655 at index 20301 0 0 seed=1662639010
lh-Diff-Ayahuasca-Control-Intercept-volume
maxvox sig=-3.05447 F=12.9196 at index 64976 0 0 seed=1662639010
lh-Diff-Ayahuasca-Control-Cor-volume-lh_cingul-ant_volume
maxvox sig=3.00408 F=12.6325 at index 130687 0 0 seed=1662639010
mri_glmfit done
mri_glmfit --y
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
--fsgd
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hand.fsgd
--glmdir
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
--surf fsaverage lh --label
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-volume-lh_cingul-ant_volume-Cor.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Cor-volume-lh_cingul-ant_volume.mat
gdfRead(): reading
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hand.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done
Continuous Variable Means (all subjects)
0 lh_G_cingul_Ant_volume 4311.07 588.108
Class Size and Means of each Continuous Variable
1 GroupAyahuasca 22 4295.8182
2 GroupControl 22 4326.3182
INFO: gd2mtx_method is dods
Reading source surface
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65417.000000
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195472
7.2.0
cwd
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
cmdline mri_glmfit --y
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
--fsgd
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hand.fsgd
--glmdir
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
--surf fsaverage lh --label
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-volume-lh_cingul-ant_volume-Cor.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Intercept-volume.mat
--C
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Cor-volume-lh_cingul-ant_volume.mat
sysname Linux
hostname Zenbook
machine x86_64
user psychedelic
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
logyflag 0
usedti
FSGD
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hand.fsgd
labelmask
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
maskinv 0
glmdir
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
Loading y from
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/Xg.dat
Computing normalized matrix
Normalized matrix condition is 417.412
Matrix condition is 2.034e+09
Found 148151 points in label.
Pruning voxels by thr: 1.175494e-38
Found 146665 voxels in mask
Saving mask to
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/mask.mgh
Reshaping mriglm->mask
search space = 72932.786449
DOF = 40
ERROR: MatrixResidualForming(): X is not invertable
RD is not invertable n = 1
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