FreeSurfer Error: Runtime Error and mpr2mni305 Error

Hi everyone!

I have tried to run fmriprep on Linux and have come up with the following error (file attached below). I’m unsure if I understand what it means, so I thought I’d ask here. Here are some background details that may be needed:

fmriprep-docker version: 21.0.2
Data is BIDS validated
Command: fmriprep-docker ~/Desktop/AJ_3 ~/Desktop/AJ3_Output participant --participant-label 01 --fs-license-file ~/Desktop/license.txt -w ~/Desktop/scratch
Run on Linux Server

If anyone knows how to solve this error, let me know! Thank you.


crash-20220803-171141-root-autorecon1-de75ac02-7871-4323-b6ca-98998ae66e98.txt (14.5 KB)

Hi Akshaj,

Are your data BIDS valid? Also, can you attach the recon all log crash file that is referenced in the log you attached in your first post?


Hi Steven,

Yup my data is BIDS valid. Here is the recon file from my first post. The one from my first post was run on Windows, whereas the one that I have attached in this post is run on a virtual Linux server.

File from old
crash-20220719-173609-root-autorecon1-e61254b6-5679-40e3-86ae-5a1c2dff0f5d.txt (4.5 KB)


I was referring to the file referenced by the lin: For more details, see the log file /out/sourcedata/freesurfer/sub-01/scripts/recon-all.log

Good to know the data are bids valid.


Sorry about that! Here’s the file. I converted it to a .txt file so that I could upload it here.

recon-all.txt (27.2 KB)