Freesurfer v.6 on Neurodesk

[PaigeHowell]

Hello! :)

I was wondering if it is possible to run Freesurfer version 6 through Neurodesk? I have installed Freesurfer version 7.4.1 via Neurodesk on a HPC. However, I am following the HCP fMRI analysis pipeline, which is designed to be run on Freesurfer version 6. When running the HCP pipelines with FS 7.4.1 there are minor incompatibility issues with the tkregister version. I also came across an HCP forum discussion where the HCP team mentioned that surface placement in FreeSurfer 7.x is not yet at the same quality level as in FreeSurfer 6.

Is it currently possible to access or install a FreeSurfer 6 container via Neurodesk, or is there a recommended workaround for running HCP-style bash pipelines on Neurodesk?

Thanks very much for your help!

[stebo85]

Dear @PaigeHowell - yes, it would be possible to add an older version of Freesurfer to Neurodesk. The only challenge is that someone needs to figure out how to build the older version and contribute it via the recipe system here: https://neurodesk.org/neurocontainers-ui/#tab=recipe-fm233m

[stebo85]

Dear @PaigeHowell - can you try this version and let us know if everything works as expected? curl -X GET https://neurocontainers.neurodesk.org/freesurfer_6.0.1_20260107.simg -O singularity shell --overlay /tmp/apptainer_overlay freesurfer_6.0.1_20260107.simg

[PaigeHowell]

Dear @stebo85 - thanks for your quick response and help. I tried fetching the FreeSurfer 6.0.1 image both on my HPC and locally, but the URL returns HTTP/2 403 from CloudFront/S3. So curl only downloads a ~111 byte AccessDenied XML, and Singularity then says “image format not recognised”. Is the object perhaps not publicly readable, or am I missing a required access step?

I also just happened across a complete HCP pipelines container image on the Storrs HPC system, which has FreeSurfer 6.0.1. I quickly tested this, and it seems to be working.
Thanks again for your help!

[stebo85]

Dear @PaigeHowell - can you try again? I am sorry, the file wasn't quite uploaded yet, but it is now complete:

curl -X GET https://neurocontainers.neurodesk.org/freesurfer_6.0.1_20260107.simg -O singularity shell --overlay /tmp/apptainer_overlay freesurfer_6.0.1_20260107.simg

[PaigeHowell]

Dear @stebo85 - No problem, I was able to successfully download and test it now. The main tools seem to work as expected (i.e. recon-all, tkregister2, mri_convert). The only issue I ran into was when launching freeview, which fails with:
freeview.bin: error while loading shared libraries: libQtScriptTools.so.4.
But access to this GUI is not really essential for running the pipeline.