[FieldTrip] Help on the ft_postfreesurferscript.sh Tutorial

[Michael Houston]

Hi Jan-Mathijs,

Thanks for the clarification on the tutorial! I believe my installation of
HCP-Workbench is correctly installed, as I can run the wb_view command
successfully. If I understand correctly,  the ft_postfreesurferscript.is
appropriate only for Donders Institute users. In this case, how would I go
about downsampling my cortical meshes in a way that is compatible for
Fieldtrip toolbox on a personal machine?

Thanks,
Michael


On Tue, Apr 16, 2024 at 2:22 AM Schoffelen, J.M. (Jan Mathijs) via
fieldtrip <fieldtrip at science.ru.nl> wrote:

> 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> 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
> MSBE '20, University of Houston
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C98dfcc22fd2943af2c2f08dc5de5ed88%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638488489301712596%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=JsiqIT29tG54%2BnRSRR06INobeU98eYMZAsa%2FAxYMrsk%3D&reserved=0>
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20240416/e3c01d28/attachment.htm>