Summary of what happened:
Hey everyone,
I am running fMRIPrep for preprocessing my fMRI data but I am facing issues that I can not seem to figure out.
I have set up my BIDS dataset correctly & am using the standard fMRIPrep command with Docker/Singularity. The pipeline starts fine but then I hit errors related to brain extraction and alignment. the outputs look weird—either the skull-stripping fails or the normalization looks off. I have tried tweaking a few options but no luck so far.
I came across a discussion in an AWS DevOps Training session where someone mentioned container-related issues affecting fMRIPrep. Could there be something I am missing in my Docker/Singularity setup? Has anyone else faced similar problems? There are any tips. Please share with me Also i have see this Preprocessing multi-echo fMRI data by fmriprep amd Tedana still need help.
Thank you… 
Command used (and if a helper script was used, a link to the helper script or the command generated):
PASTE CODE HERE
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
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