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fmri-preprocessing - Preprocessing of raw functional MRI


The pipeline is almost ready. Complete documentation and final pipeline version will be available soon!

This pipeline performs the preprocessing of fMRI images. This includes : head motion correction, slice-timing correction, unwarping, spatial normalization, coregistering and spatial smoothing.


If you only installed the core of Clinica, this pipeline needs the installation of SPM on your computer; and depanding on your options, the software FSL might be required or the execution of the Clinica pipeline t1-freesurfer-cross-sectional. You can find how to install these softwares on the third-party page.

Running the pipeline

The pipeline can be run with the following command line:

clinica run fmri-preprocessing bids_directory caps_directory

  • bids_directory is the input folder containing the dataset in a BIDS hierarchy.
  • caps_directory is the output folder containing the results in a CAPS hierarchy.

If you want to run the pipeline on a subset of your BIDS dataset, you can use the -tsv flag to specify in a .tsv file the participants belonging to your subset.


Results are stored in the following folder of the CAPS hierarchy: subjects/sub-<participant_label>/ses-<session_label>/fmri/preprocessing.

It contains the following files:

  • *_bold_confounds.tsv:
  • *_bold_space-Ixi549Space_fwhm-<kernel_size>.nii.gz: Smoothed version of the file below.
  • *_bold_space-Ixi549Space.nii.gz: Preprocessed fMRI data in Ixi549 (MNI) space.
  • *_bold_space-meanBOLD.nii.gz: Preprocessed fMRI registered to the mean BOLD image.
  • [optional] *_bold_space-T1w.nii.gz: Preprocessed fMRI registered to the T1.
  • *_brainmask.nii.gz: Brain mask used to register the fMRI.

(where * stands for sub-<participant_label>_ses-<session_label>)

Describing this pipeline in your paper

Example of paragraph:

These results have been obtained using the fmri-preprocessing pipeline of Clinica ( Slice timing correction, motion correction [and unwarping] have been applied using SPM tools. Separatly the brain mask has been extracted from the T1 image of each subject using [FSL | FreeSurfer]. The resulting fMRI images have then been registered [to the brain-masked T1 image of each subject | to the MNI space | to the mean image of each subject] using SPM's registration tool.