00 - from DICOM to GLM

Overview about how to get from DICOM files from the Scanner to your GLM Analysis
Author

MG

Published

March 8, 2025

1 This Site is currently under construction!!

2 General

This page gives an overview and brief information about the necessary steps to get from the DICOM files to a GLM Analysis. You can find more detailed information by navigating to the sub-pages by clicking on the caption of the respective point.

3 DICOM-Files

  • the raw files from the scanner are DICOM-Files
  • not really useful since we need .nifti files for our analysis \(\qquad\to\) first step is to transform the DICOM- to .nift-files

4 DICOM to nifti

  • using a script from Adam that can be found here (or under ADD THE PATH TO SHARED?)
  • results in .nifti files in BIDS format

5 Distribute the T1w files to participants?

  • if you promised participants that they will get their T1w images, you should make sure that they really get them
  • this should be done before defacing

6 Defacing your data

  • \(\bf{You\ have\ to\ deface\ your\ data\ before\ running\ fmriprep\ or\ your\ analysis!!!!!}\)
  • You may want to save the “non-defaced” files somewhere else to give them to your participants
  • You should delete the “non-defaced” files either after you distributed them to the respective participants, or after your study ended
  • NEVER share data that was not defaced before!
  • Defacing is done with pydeface (Docker; Version 2.0.2)

7 (Remove denoising scan from your data)

  • if a denoising sequence was used in the scanner, but you don´t use denoising in your analysis, you have to remove the last volume of each scan (which basically is a noise scan) before continueing

8 fmriprep

9 first-level Analysis