Hi Paul, I started to play with obliquity_remover.py , and It sounds useful to apply this to EPI data, as it preserves the original correspondence with the T1w image. May I ask two questions: I assume that, if I use the blip up/down method for distortion correction, it is better to treat the AP …

Hi again, @zhengchencai - Re. your second question, as to what has obliquity or not after running obliquity_remover.py: Let's assume that AAA.nii.gz has obliquity (so, 3dinfo -is_oblique AAA.nii.gz produces 1). If you run the following to remove obliquity from AAA.nii.gz and to append it to child…

I tested on an old dataset. 3dinfo -is_oblique func/*_run-1_bold_DEOB.nii.gz return me 1, is this expected? Please find the detailed code below > 3dinfo -is_oblique anat/sub-ep0568_T1w.nii.gz 1 > 3dinfo -is_oblique func/sub-ep0568_task-spike_run-1_bold.nii.gz 1 > obliquity_remover.py -inset anat…

Hi, @zhengchencai : I'm running out the door, but could I just ask what your AFNI version is (afni -ver), re. the speed issue? --pt

Hi @ptaylor , no rush at all, just want to provide some test feedback. > afni -ver Precompiled binary macos_13_ARM: Dec 24 2025 (Version AFNI_25.3.04 'Gordian II') Here is my afni_system_check.py -check_all output -------------------------------- general --------------------------------- architect…

Hi, @zhengchencai : Thanks for the version info. That is uptodate; some changes had been made prior to that to speed it up for the QC images. To Q1 above: for the majority of volumetric FMRI processing, users want the EPI data to end up either in participant's own anatomical dataset space (like…

Hi @ptaylor , Thanks for the very detailed explanation, now I understand obliquity_remover.py better. I also figured out why QC was not working (the example I mentioned was 5mm fMRI). It seem it was because I did not install ffmpeg. My XQuartz was up to date and was working fine for AFNI GUI and a…

Hi, @zhengchencai - Great, glad to know that was useful, and that the runtime+QC image issue was resolvable. That is interesting about ffmpeg resolving that error. That is /tmp/.X11-unix is a known (and annoying) issue on Macs, when running Xvfb (which @chauffeur_afni does). There is this troubl…

Hi @ptaylor , Indeed you are right. It was not solved by ffmpeg, I rebooted and the error was back. Then I recall that I did open AFNI GUI before running obliquity_remover.py. I did the command you sent it worked but the error was back after rebooting, as tmp was gone. I guess I will just set XQuar…

Hi, @zhengchencai - Ah, that's a great idea to make Quartz a startup app! Nice. --pt

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