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Dear FreeSurfer Team,
As part of the ENIGMA consortium, research groups that contribute data need to run certain standardized scripts to pre-process their data and create outputs for subsequent quality control using FreeSurfer.
One issue that has recently occurred is that Mac users with a recent MacOS are no longer able to run one of the scripts that uses tksurfer to generate lateral and medial screenshots of the pial surface reconstructions. Reading previous posts in the mail archive, this seems to be due to recent versions of MacOS being unable to run 32-bit programmes like tksurfer and that users should either use Freeview for visualisation or revert to an older operating system.
As the latter is not possible for some groups, we’ve been trying to edit the script by altering which programme it calls (e.g., freeview or tksurferfv instead of tksurfer) as well as other aspects of the script (e.g., -cmd instead of -tcl). However, so far, we have been unable to successfully amend the script.
Would you have any pointers for us as to how to alter the script to call freesurfer whilst arriving at the same output (i.e., multiple screenshots of the external view of a subject’s brain)? Is there a way to script Freeview similar to using tcl in tksurfer?
I have also attached the script in question to this email. The FreeSurfer versions used by the contributing research groups are 5.3 or 6.0.
Thank you in advance for any advice you might have on this.
Best wishes, Marlene