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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** #2561

Open Avijit-Chowdhury1 opened 3 years ago

Avijit-Chowdhury1 commented 3 years ago

Trying to preprocess one subject with multiple sessions of data and fmriprep crashes with the following error.

crash-20210925-192047-achowdhury-autorecon1-b29726d6-d970-4f9c-a68d-8cedaaf96df3.txt

My data is 7T so there might be a need for bias field correction - I am not sure if it is already included within fmriprep workflow. Here is the data: https://www.dropbox.com/sh/n9qwvyjz573tt27/AABrEo53XCAiYgk64GxwtdwTa?dl=0

Thanks!

effigies commented 3 years ago

Are you able to run this dataset through freesurfer independently?

Avijit-Chowdhury1 commented 3 years ago

Nope getting the same error running recon-all command by itself

Avijit-Chowdhury1 commented 3 years ago

solved: run bias field correction of 7T T1 images before feeding it to fmriprep. Instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon

Could this be included as part of fmriprep workflow in the future?