MRI-Studies: General Information

MRI
Useful information to consider before and while doing a (f)MRI Study
Author

MG

Published

July 21, 2025

This page is a constant work-in-progress file. The goal is to gather and provide necessary/useful/helpful information regarding (f)MRI studies. It can serve as a helpful guide when starting to plan an Experiment and while doing it. If you already acquired your data, you can refer to this page for information about the processing and analysis of your data.

If you realize something that is missing, please let us know, so we can add it here!

1 Planning a study

1.1 events.tsv files

  • to save time later, keep in mind that you often need *_events.tsv files for your analysis! see here

  • In our fMRI Studies, the bare minimum generally is that these files should include is the Onset, duration and trial_type (e.g. the condition that was shown). This is later used to build your contrasts, e.g. in the first level GLM

  • *_events.tsv files have to be named exactly like the functional run they are referring to (except the ending). E.g. for the functional scan sub-140001_ses-1_task-loc_run-01_bold.nii.gz, the corresponding file has to be named sub-140001_ses-1_task-loc_run-01_events.tsv

Example of a rudimentary .tsv file:

onset   duration    trial_type
0.5     1.0         Condition A
2.0     1.0         Condition B
4.0     1.5         Condition A

2 Piloting a study

  • when you do a pilot run with Natalia, you might get the raw DICOM files. Load them to the server and delete them as soon as possible from any external device (USB-Stick, local storage of your computer, etc.)

3 Running a study

  • When a study starts, you should save the sequence that is used for data acquisition. This can be useful for your thesis/paper, or for other studies in the future. Just ask Thomas or Alex to save the sequence as a PDF. If you have access, save this PDF to storage/nv_shared/Neurovision_Protocols (if you don´t have access, send it to Natalia)

  • make sure that your participants completely understand what will happen and what they´ll have to do in the scanner!!! If participants have to do a task while they are in the scanner, explain to them in detail what they have to do! Reassure that everything is clear by asking back! Include short reminders of the task before each run (if applicable). Only if participants understand what they have to do, we can get the data that you want (or what the study was designed for). It can also help to have a demo-run ready on your laptop to show participants what will happen (there are also computers at the MRI-Lab that could be used for this. If you want to use them, test it first!)

  • If you compensate participants, carefully read the corresponding entry

  • At least after the first functional run (or after every run) of your experiment (or after the anatomical scan), do a visual “assessment” of the participants movement. Just ask Thomas/Alex to do this, they should know what you mean. If this inspection reveals, that participants moved too much, you can re-instruct them to don´t move. This can potentially avoid getting data at the end, that are unusuable due to huge movement artifacts. (You may do a detailed quality control at the end with MRI QC)

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