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What am I trying to do:
I am trying to register my functional resting state scan to the MPRAGE scan (which is saved in the freesurfer subjects directory under ‘subject _30_8_2020’ after running recon-al on a MPRAGE that was aligned to AC PC). The mgz file brain.mgz and the functional scan aligned.
What are the commands I use
bbregister --s subject_30_8_2020 --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.dat --init-header –bold
tkregisterfv --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat –surfs
(bbregister works, tkregisterfv does not; I only provide the bbregistercode for context)
What is the error?
When I try to run tkregisterfv, I get the following output:
“cd /Users/me/Documents/30_8_2020/subject_REST_CF
freeview -transform-volume -viewport cor -v /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/mri/orig.mgz:visible=0:name=orig.mgz(targ) /Users/me/Documents/30_8_2020/subject_REST_CF/subject_motion_corrected_func_4D_RestingState.nii:name=subject_motion_corrected_func_4D_RestingState.nii(mov):reg=/Users/me/Documents/30_8_2020/subject_REST_CF/affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat --surface /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/lh.white:edgecolor=yellow --surface /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/rh.white:edgecolor=yellow
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary operator expected
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN'
/Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'”
My platform:
macOS Mojave, version 10.14.6
There is no recon-al log.
What I tried to do/ checked:
1) FSL is installed.
2) the fsvglrun text describes fsvgl as a necessary file, and I found that VirtualGL is supposed to contained that, and I tried to install that. It also says that FS_ALLOW_VGLRUN should be set to 1, but I have no idea how to do that.
3) make sure to reboot after every potential solution.
None of that worked/ resolved the issue.