External Email - Use Caution I’m not sure it will make a difference, but you could try downloading, installing and running one of the current development builds for the Silicon Mac. You could try this download link, https://secure-web.cisco.com/1knximumtc7HGhko0zDsKDfS2Nqhp3y3blHXGS-mPKcRQ-2luavC6Mq9rvDUJYmUM_VbyhxAAIBhGwI31zlmxUtqwDUNwa4YthPxUvazsca50xAOHgKTqwZiT6-xSv-TigJXP41F06y1wQ2hv5FQINurFhlYJSd3kvnYeiKf3yr-H9mJQgLpuJeTgYsb9w5GRt9VWSpFSYvgj38dbu76zQiUysDyRGMKr9EJ8QN6S2z9adVQ21A7L5-tsy90yaWA3WUmhVR180cvBo6m3TNg0LZFnYHWbh2Fd1YzjuBjEpgQqGOWnytWPYTIbzKjhngHS/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2Ffreesurfer-macOS-darwin_arm64-dev.pkg - R.
On Oct 4, 2024, at 12:20, Shawn Flanagan <shawn..flana...@rosalindfranklin.edu> wrote: 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_64-7.4.1-20230614-7eb84602) Platform: Mac Studio M23) 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, PhDAssociate ProfessorDirector, Human Performance LaboratoryDepartment of Podiatric Medicine and SurgeryDr. William M. Scholl College of Podiatric MedicineNeuroscience ProgramSchool of Graduate and Postdoctoral studiesshawn.flana...@rosalindfranklin.edu <CON-ACLleft.mtx><CON-ACLright.mtx><CON-ACLtar.mtx><mri_glmfit.log><BBACL.fsgd><runGLMs.sh>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1UTFsfZM2c36YeGLIQ25Bild7hRzYEEJsr_HuaallFxuHtnUbKv7yQmyGHUSt5-0vlKU5m0d7AsdsdbyFW00LH0Pz7VkETzVtPLMYHJfIrPTpn3-BTz09gXdcTVUaqVGeqeKAGZ086u7XcPswwt3Zin3qSyctMbIT7nqHOff5bEfsaXP340LMySLWoIHhvsuYFMik8ldCqH8TtHp6rCgUcXgvozc2glO0PY4Tx3BYwgxmkPNt_aLin-gVUqMRpI3C3W6FXDVtk4qc3ai8DmXBr2UorD1SuFTLkevV_Ktu-F0Z-6fdzNUG03kPcRmDLdLb/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.