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_directoryis the input folder containing the dataset in a BIDS hierarchy.
caps_directoryis 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:
It contains the following files:
*_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.
*_bold_space-T1w.nii.gz: Preprocessed fMRI registered to the T1.
*_brainmask.nii.gz: Brain mask used to register the fMRI.
* stands for
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.