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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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including non-brain func data in registration #2753

Open manzouri opened 2 years ago

manzouri commented 2 years ago

What happened?

I run fmriprep on the subjects with 5 sessions and having 4 tasks per session. In the report of Alignment of func and anat MRI , there are both volume and surface driven results and for the majority of tasks and sessions , it seems that anat has been registered to func data including non-brain regions. I can also see maybe 1 out of 20 good registration in one subject. I plan to use the confounds and denoise the data and then register it to MNI 3mm and feed it to another program. So I would like to know if the alignment affect my steps ( ie. on confound calculations) and also the reason of the poor alignment.

What command did you use?

fmriprep-docker $bids_root_dir $out_dir/ \
    participant \
    --participant-label $subject \
    --skip-bids-validation \
    --md-only-boilerplate \
    --output-spaces func:res-native \
    --bold2t1w-dof 12  \
    --fs-license-file /usr/local/freesurfer/license.txt \

What version of fMRIPrep are you running?

fMRIPrep version: 21.0.1

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

sc1 sc1-1 sc2

effigies commented 2 years ago

Your bold-T1w degrees of freedom is 12, which is very rarely needed. It looks like you're seeing scaling issues, as your BOLD is significantly smaller than your T1w. I would suggest retrying with 6dof and seeing if you get better results.

The coregistration should have no impact on confounds.

manzouri commented 2 years ago

Hi and thanks @effigies , do you have any recommendations for denoising also , tool and which confounds?