On Oct 4, 2024, at 12:20, Shawn Flanagan <shawn.flanagan@rosalindfranklin.edu> wrote:

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Hi FreeSurfer Developers,

I am attempting to compute group analysis as described in the FS tutorial and it appears to run but with the following message at the end for each contrast:

Writing results
  CON-ACLleft
    maxvox sig=-2.57471  F=9.30914  at  index 155198 0 0    seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13..2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
  CON-ACLright
    maxvox sig=2..75772  F=10.1304  at  index 31842 0 0    seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4..13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
  CON-ACLtar
    maxvox sig=2.22177  F=7..75177  at  index 69873 0 0    seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13..2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18
mri_glmfit done

I have searched the list and no similar errors have been reported. Does anyone have thoughts or insights about this? If it is helpful, I have attached the fsgd file, contrast files, script file, and a representative mri_glmfit log file. 

1) FreeSurfer Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460

2) Platform: Mac Studio M2

3) Script: 

#!/bin/tcsh

set study = $argv[1]

foreach hemi (lh rh)
  foreach smoothness (0 5 10 15 20 25)
    foreach meas (volume thickness)
        mri_glmfit \
        --y ${hemi}.${meas}.${study}.${smoothness}.mgh \
        --fsgd FSGD/${study}.fsgd dods \
        --C Contrasts/CON-ACLleft.mtx \
        --C Contrasts/CON-ACLright.mtx \
        --C Contrasts/CON-ACLtar.mtx \
        --surf fsaverage ${hemi} \
        --cortex \
        --glmdir ${hemi}.${meas}..${study}.${smoothness}.glmdir \
        --eres-save
    end
  end
end

Appreciate your time and advice!

Best,

Shawn

-- 

Shawn Flanagan, PhD

Associate Professor

Director, Human Performance Laboratory

Department of Podiatric Medicine and Surgery

Dr. William M. Scholl College of Podiatric Medicine

Neuroscience Program

School of Graduate and Postdoctoral Studies

shawn.flanagan@rosalindfranklin..edu

<CON-ACLleft.mtx><CON-ACLright.mtx><CON-ACLtar.mtx><mri_glmfit.log><BBACL.fsgd><runGLMs.sh>_______________________________________________
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