Output data shape

[Bwertle]

Hi,

Very new to the neuro-imaging field. I've tried using your tool on bold fMRI data that I pre-processed with fmriprep however in the output files the data no longer resembles a brain but is cuboid instead. Is there a parameter I'm missing?

Thanks.

[kbonna]

Hi,

did you get any errors? Denoising is not applying any volume transformation, so this should not happen. Can you send sample image before and after denoising?

[Bwertle]

Hi,

Thanks for replying so quickly. I didn't get any errors during the run.

This is part of my honours project and the data is bound by ethics so I can't send any sample input images at this stage but I've attached a volume from the output.

I also noticed however that while I can view the input (output from fmriprep) in FSLeyes an error occurs when attempting to view the output in FSLeyes, I'm only able to view individual volumes using MRIcroGL. I'm not sure whether this is a related issue.

I can confirm that the inputs are non-skull stripped pre-processed bold-signals from fmriprep.

[manzouri]

Hi,
I also ran fmridenoise on 2subjects and did not get any error. But the output looks like this

[SiegfriedWagner]

Have you used fmriprep before using fmridenoise?

[manzouri]

Yes.