bids-apps / tracula

implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Not finding freesurfer reconstructions from fMRIprep-generated freesurfer directory

bwinsto2 opened this issue · comments

Hello,
First of all, thank you for making this app. I've already run fMRIprep on my dataset, which ran freesurfer recon-all. fMRIprep generates /derivatives/freesurfer, so I passed this to the freesurfer_dir argument:
docker run -ti --rm \ -v /data2/1305/raw_data:/bids_dataset:ro \ -v /data2/1305/derivatives/tracula:/outputs \ -v /data2/1305/derivates/freesurfer:/freesurfer \ bids/tracula \ /bids_dataset /outputs participant --participant_label abc123 \ --license_key "CIBCuo9p/WEY" \ --freesurfer_dir /freesurfer
Yet after running this, I get the message: 'Freesurfer for abc123 not found. Running recon-all'. Any ideas why this could be the case? The GIfTI files themselves are in the /derivatives/fmriprep/sub-abc123/anat folder--are these what tracula is looking for? I tried the same code above but with /derivatives/fmriprep as the freesurfer directory instead, and that didn't work either. Worst case, I could just run recon-all again, but it would be unfortunate since I just ran fMRIprep on these data.
Thanks very much @chrisgorgo and/or @fliem :)

The code in the examples on the Github page spell derivatives wrong. This was my problem since I copy/pasted some of the code.