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Hello Peter,

This thread was made 3 months ago, but I post additional information here. Hope it will help anyone who meets the same issue.

My environment is almost same as yours (FS ver. 7.1 on macOS Mojave), and I experienced the same error.
Version of bash seems the cause. The “-v” option of “test” command in bash is implemented in bash later than ver. 4.2. Indeed I could solve the issue by installing newer bash.
Please don’t forget to change shebang of fsvglrun if you install new bash in other path than /bin/bash!

Best regards,

Takahiko

On 12/20/2020 5:03 AM, Peter de Best wrote:












        External Email - Use Caution












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.




































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