Overview - from DICOM to GLM

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

1 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.

2 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

3 DICOM to nifti

• using a script from Adam that can be found here (or here: /shared/dcm2bids.sh)
• results in .nifti files in BIDS format

4 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

5 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)

6 (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 continuing

7 fmriprep

• this is one of many BIDS-Apps (that require a BIDS-valid Dataset)
• runs various preprocessing steps on it´s own

8 first-level Analysis

9 second-level Analysis