Incorrect ICA_AROMA outputs

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1

Summary of what happened:

I accidentally deleted some of my denoised_func_data.nii.gz files from my ICA_AROMA output. I have tried to rerun my ICA_AROMA script thinking this will be a simple fix, however when I run my code this time it is outputting everything except the denoised_func_data.nii.gz file, including the denoised_func_data_nonaggr.nii.gz file. I have no idea what is going wrong, and have tried to rerun the code in different directories, and have manually added the mask etc and it still doesn’t output the denoised_func_data.nii.gz file. There are no errors that come up that I can see. Any help would be really appreciated as I’m new to this type of analysis. This is the code I’ve been using:

Command used (and if a helper script was used, a link to the helper script or the command generated):

    fsl_sub -N aroma_${subj}_${timepoint} ICA_AROMA -f "~/scratch/RS/${subj}/${timepoint}/preprocess.feat" -o "~/scratch/RS/${subj}/${timepoint}/preprocess.feat/AROMA"

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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Screenshots / relevant information:

2

Hi there,

I might be completely mistaken, but it looks like ICA-AROMA is actually running as expected. The output filenames depend on the denoising strategy used.

When ICA-AROMA is run in non-aggressive denoising mode (which is often the default), it produces denoised_func_data_nonaggr.nii.gz. When aggressive denoising is enabled, ICA-AROMA instead produces denoised_func_data.nii.gz (without the suffix).

Since you are getting the _nonaggr file without errors, this suggests ICA-AROMA completed successfully. If you previously had a plain denoised_func_data.nii.gz, it was likely generated during an aggressive run or renamed by a helper script or manual step.

If your downstream scripts expect that specific filename, you can rename the file (noting that this does not change the denoising strategy):

denoised_func_data_nonaggr.nii.gz denoised_func_data.nii.gz

Otherwise, using the _nonaggr file directly is typically the recommended approach for resting-state analyses.

Also since you are using fsl_sub, any actual errors will not appear in your terminal window. They will be written to log files in the directory where you ran the command.
It is worth checking those .e files just to be sure there were no hidden permission errors, though the presence of the _nonaggr file suggests the job ran successfully.

Hope that helps :slight_smile: (I’m sorry if it doesn’t)

3

Great, thank you so much. I didn’t know that _nonaggr file was the standard approach for resting state so that should be fine.

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