Fmriprep ica aroma

Hi everyone,

I am wondering how to adjust the ICA Aroma clean up with fmriprep’d data.

After using the --use-aroma tag I then reviewed the reports and I noticed that some components were classified as signal that should have been labeled as noise. Is it possible to add those components to the func/sub-<subject_label>_[specifiers]_AROMAnoiseICs.csv file and then somehow adjust the denoising step by using fsl_regfilt? If so which image do we apply this to?

I found this on the fmriprep website:

Additionally, the MELODIC mix and noise component indices will be generated, so non-aggressive denoising can be manually performed in the T1w space with fsl_regfilt , e.g. :

fsl_regfilt -i sub-<subject_label>_task-<task_id>_bold_space-T1w_preproc.nii.gz \ -f $(cat sub-<subject_label>_task-<task_id>_bold_AROMAnoiseICs.csv) \ -d sub-<subject_label>_task-<task_id>_bold_MELODICmix.tsv \ -o sub-<subject_label>_task-<task_id>_bold_space-_AromaNonAggressiveDenoised.nii.gz

However the sub-<subject_label>_task-<task_id>_bold_space-T1w_preproc.nii.gz file is nowhere to be found in my output files. Any help would be appreciated!

Thank you

cc @jdkent

If you’re using recent fMRIPrep (1.2.0+), then the name will be sub-<subject_label>_task-<task_id>_space-T1w_desc-preproc_bold.nii.gz.

Thank you,

I am using fmriprep-docker version 1.5.0.

The T1w doesnt exist for some reason so I am now attempting to rerun it with --output-spaces T1w to see if it gives me the file with that command.

Hi @JustinAndrushko,

The documentation was outdated for the filenames, thank you for pointing this out, I just created a pull request to change this.

Yes, this method is possible, I would only recommend that you create a new file perhaps called sub-<subject_label>_[specifiers]_desc-edited_AROMAnoiseICs.csv so you do not overwrite the existing output. The only other note is that whatever image you pass into fsl_regfilt will not be spatially smoothed (the non-aggressively denoised outputs from fmriprep are smoothed). You do not need to the T1w output space, that was only the example provided, so you can choose whatever space you generated in your fmriprep output (e.g., “MNI152Lin”, “MNI152NLin2009cAsym”, “MNI152NLin6Asym”, “MNI152NLin6Sym”, “MNIInfant”, “MNIPediatricAsym”, “NKI”, “OASIS30ANTs”, etc.).

Please let me know if you have further questions!