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Hi Ruopeng,
You were correct - for some reason the version I built was 2.0. I’ve downloaded a built version of freesurfer v7.1.0 and now I can successfully use the flag.
Another question if I may: is there a way to toggle the “clear lower”/“clear higher” option also from the terminal?
Thank you in advance! Best regards, Ricardo
Date: Thu, 18 Jun 2020 13:28:56 +0000 From: "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview - Load custom overlay from terminal To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <FE2C8592-CFC2-41FD-9BB0-B4763CA86185@mgh.harvard.edumailto:FE2C8592-CFC2-41FD-9BB0-B4763CA86185@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"
Hi Ricardo,
The way you use the flag is correct. But have you made sure that you were actually running the latest version that you built? You can check freeview?s build time from About menu.
Best, Ruopeng
Date: Thu, 18 Jun 2020 08:15:44 +0000 From: "Loucao, Ricardo" <r.loucao@fz-juelich.demailto:r.loucao@fz-juelich.de> Subject: [Freesurfer] Freeview - Load custom overlay from terminal To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <25D279E0-2256-47B0-B05A-1F470A1B3089@fz-juelich.demailto:25D279E0-2256-47B0-B05A-1F470A1B3089@fz-juelich.de> Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear FS experts,
I?m trying to load a surface with a custom overlay directly from the terminal using the sub-option ?overlay_custom? but it returns ?Unrecognized sub-option flag ?overlay_custom??. I checked the source code on GitHub and found the flag to be present and implemented. I also built the freeview app from the GitHub (as it could be that my version did not have that sub-option) but I got the same return message.
Upon inspecting the code further, I figured the way this flag works is via quadruplets of the form ?val, r, g, b?. However, I also noticed that this return message comes when the overlay_custom sub-option is empty (freeview/MainWindow.cpp: line 3484). It seems to me like I might be using the flag improperly. Here?s an example of how I am using it: ?:overlay_custom=0.85,255,0,0,0.875,0,255,255,0.90,0,0,255?
Do you have any hints for me on how to deal with this?
Thank you very much in advance! Best regards, Ricardo
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