Using Clinica on "raw" MRI data (original scans) or need for preprocessing before ?

[Mathilde Bateson]

Hello Clinica experts !

I will be trying to use Clinica on ADNI but also on other data which has not been preprocessed / normalized, etc but instead "raw data".

Question : can I use Clinica on raw brain MRI images or do I need a preprocessing pipeline before to harmonize the data, remove acquisition artefacts etc...

For ex Combat ? sthg else ?

The goal of using freesurfer is to extract the hippocampus volumes.

So the question is : are the volumes going to be erroneous if I don't do some harmonisation/ preprocessing ? How erroneous ? 10% ? 100% ? Is there literature on this ?

Thanks ! 

Mathilde

[ninon....@gmail.com]

Hi Mathilde,

The pre-processing pipelines available in Clinica include correction of some acquisition artefacts such as intensity inhomogeneities but not others, such as motion artefacts.

Harmonisation is another consideration that is not addressed by Clinica. Tools such as Combat allow you to harmonise extracted features (e.g. hippocampal volumes), but not whole images.

If your objective is to use FreeSurfer, have in mind that this tool is sensitive to image quality. If the image is of too poor quality, the processing may fail or lead to erroneous extracted volumes.

Hope this helps.

Best,

Ninon