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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 M 36.767 1046505.93 25 Input 102 F -58.589 955597.34 30 Input 103 M 68.883 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