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-2... - R.
On Oct 4, 2024, at 12:20, Shawn Flanagan <shawn..flanagan@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.flanagan@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_HuaallFxuHtn...
External Email - Use Caution
Hi,
This doesn't make a difference. I can say that the Apple M- dev version likely has an issue with the permutation procedure in runClustSims.sh. At the GLM stage, the program is still saying that the matrix is rank deficient by the number of matrix entries (18).
Best, Shawn
On Sat, Oct 5, 2024 at 9:38 PM fsbuild fsbuild@contbay.com wrote:
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://surfer.. nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/stable/freesurfer-macOS-darwin_arm64-dev.pkg
- R.
On Oct 4, 2024, at 12:20, Shawn Flanagan < shawn.flanagan@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_64-7.4.1-20230614-7eb8460* *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 shawn.flanagan@rosalindfrankln.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/15-QCjfZbC6gZSi5uu4p6rFByNO8jhfMeWJUBBfYsQPjldw...
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Shawn Flanagan