External Email - Use Caution
*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(a)rosalindfranklin.edu <shawn.flanagan(a)rosalindfrankln.edu>