External Email - Use Caution

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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mghbRbdQp2NBhEK9y-ocIdgx-Br8K0MGsdp5VagBN8Xk2N... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mghbRbdQp2NBhEK9y-ocIdgx-Br8K0MGsdp5VagBN8Xk2N...