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:
"+0.0 +0.0 +1.0 +1.0 +0.0 +0.0 +0.0 +0.0”
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.
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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