Sorry, one of the reasons we stopped supporting QDEC was because it became impossible to debug these kinds of things. Please use the command line stream (ie, create an FSGD file and contrast matrices, run mris_preproc, mris_fwhm, and mri_glmfit). I can help you once you recreate the error

On 5/18/2020 9:07 AM, Mikael Novén wrote:

External Email - Use Caution

Dear FreeSurfer Developers,

I’m attempting to run a cortical thickness correlation analysis regressing out the effect of brain size, age and gender. However, when attempting to run this analysis in qdec (or trying to use mri_glmfit separately) I get the following error: "MatrixMultiplyD(): m2 is null  break matrix.c:415

No such file or directory”

Full output from the mri_glmfit call is last in this mail.

The first lines of my fsgd files look like this: "GroupDescriptorFile 1 Title RTfMRI Class M Class F Variables RT eICV Age Input 101 M36.767 1046505.93 25 Input 102 F-58.589 955597.34 30 Input 103 M68.883 1107660.32 22”

My contrast matrix looks like this: "+0.00000 +0.00000 +1.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000”

Any help is much appreciated.

Kind regards, Mikael

mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex --glmdir fMRIRT_revision_test2 gdfRead(): reading fMRIRT_age_gender_eICV.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 RT 82.6508 76.4669 1 eICV 980394 122148 2 Age 24.5294 3.23797 Class Means of each Continuous Variable 1 M  97.4687 1037828.2188  25.0000 2 F  74.5684 949066.0966  24.2727 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/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 /Applications/freesurfer/subjects cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex --glmdir fMRIRT_revision_test2 sysname  Darwin hostname LUMAC1089 machine  x86_64 user     root FixVertexAreaFlag = 1 UseMaskWithSmoothing     1 OneSampleGroupMean 0 y  /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh logyflag 0 usedti  0 FSGD fMRIRT_age_gender_eICV.fsgd labelmask  /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir fMRIRT_revision_test2 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory fMRIRT_revision_test2 Loading y from /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh    ... done reading. INFO: gd2mtx_method is dods Saving design matrix to fMRIRT_revision_test2/Xg.dat Computing normalized matrix Normalized matrix condition is 3815.6 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149078 voxels in mask Saving mask to fMRIRT_revision_test2/mask.mgh Reshaping mriglm->mask... search space = 74130.630564 DOF = 9 Starting fit and test Fit completed in 0.0511667 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361 Writing results   RT_covNI_cp     maxvox sig=-4.61019  F=62.3686  at  index 156731 0 0  seed=1590285961 MatrixMultiplyD(): m2 is null  break matrix.c:415

No such file or directory

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