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pnlbwh / pnlpipe-containers

Containers for pnlpipe software
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bad X server connection for WMA pipeline #24

Open kavandeloo97 opened 4 days ago

kavandeloo97 commented 4 days ago

Hi there, I get the following error when attempting to run the first step in the WMA pipeline (https://whitematteranalysis.readthedocs.io/en/latest/subject-specific-tractography-parcellation.html). I do personally have XQuartz running on my local, but I am assuming this is related to the docker. Any insight is appreciated!

(pnlpipe3) [root@49026ee06aa7 dwi]# wm_quality_control_tractography.py /home/pnlbwh/myData/test-jun16/sub-HV101/ses-01/dwi/ukf/ /home/pnlbwh/myData/test-jun16/sub-HV101/ses-01/dwi/WMA Importing whitematteranalysis package.

Starting... Found 1 subjects in input directory: /home/pnlbwh/myData/test-jun16/sub-HV101/ses-01/dwi/ukf/ Testing all files for quality control (computing fiber length measurements and rendering to make sure header and gradient orientations are ok). See the README.txt file in the output directory for more overview information. Subject 1 / 1 ID: sub-HV101_ses-01_desc-UnXc_dwi_EdEp ERROR: In ../Rendering/OpenGL2/vtkXOpenGLRenderWindow.cxx, line 452 vtkXOpenGLRenderWindow (0x55c3b7a1cc70): bad X server connection. DISPLAY=Aborted (pnlpipe3) [root@49026ee06aa7 dwi]#
tashrifbillah commented 4 days ago

Very normal. It won't run in a headless mode. You need to have GUI or GUI server for this. Install WMA directly in your Linux computer and run it there.

kavandeloo97 commented 4 days ago

Thanks. Can it be run on a Mac?

tashrifbillah commented 4 days ago

Ask whitematteranalysis folks. Sorry!