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fmri-preprocessing - Preprocessing of raw functional MRI

Note

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.

Dependencies

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
where:

  • 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.

Outputs

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 (http://www.clinica.run). 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.

Tip

Easily access the papers cited on this page on Zotero.