[FieldTrip] Help on the ft_postfreesurferscript.sh Tutorial

[Schoffelen, J.M. (Jan Mathijs)]

Hi Michael,

Sorry for the confusion. The instructions in the tutorial pertain to how the software can be run on the local filesystem of the Donders Centre. The module load command in general is useless if one is trying to run the software somewhere else. We will clarify this in the documentation. For now, you probably would want to try and install an instance of the software yourself on the compute that you are using. https://www.humanconnectome.org/software/connectome-workbench<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.humanconnectome.org%2Fsoftware%2Fconnectome-workbench&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C98dfcc22fd2943af2c2f08dc5de5ed88%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638488489301712596%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=k788VQ8xqUX9lr5UcfM9BNrSQurndPxGhAsgB0qKmVs%3D&reserved=0>

Best wishes,
Jan-Mathijs


On 15 Apr 2024, at 16:42, Michael Houston via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello! I am new to HCP Workbench and am intending to use it to downsample cortical meshes after their creation in Freesurfer to finally use them in Fieldtrip toolbox for EEG source analysis according to the tutorial in this link (https://www.fieldtriptoolbox.org/tutorial/sourcemodel/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C98dfcc22fd2943af2c2f08dc5de5ed88%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638488489301712596%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=g%2FJ5qi8NMoEQYbzQm%2BxLKd1TFXm%2FBJhlv5%2BnHtkrOnE%3D&reserved=0>).

Prior to running ft_postfreesurferscript.sh the tutorial states that I need to make sure the HCP workbench module is loaded and ready to use. However, when I run <module load hcp-workbench> I am told that the module command does not exist. After researching, it looked like I needed to enable the universe repository, which I did. Afterwards, the module command still did not work. Another search led me to look for a file under /etc/profile.d/modules.sh. However, it would appear that under Ubuntu 22.04 such a directory does not exist.

For further context, I am running Ubuntu 22.04 under WSL on a machine natively running Windows 11. If there is any other information I should provide that I missed, please let me know. Thank you!

Thanks,
Michael
--
mjhouston2 at uh.edu<mailto:mjhouston2 at uh.edu>
MSBE '20, University of Houston
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https://doi.org/10.1371/journal.pcbi.1002202

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