Before starting this tutorial#

  1. Make sure that you have the following files in your working directory:

    • single_subject/data/fmri/fmri.nii.gz : A 4D fMRI image comprised of 35 3D volumes.

    • single_subject/data/t2/t2.nii.gz : A 3D anatomical image used to create a mask around spinal cord for the fMRI image.

    • single_subject/data/t2s/warp_template2t2s.nii.gz : A warping field to transform the PAM50 template to the T2s space, informed by the shape of the gray matter.

    • single_subject/data/t2s/warp_t2s2template.nii.gz : A warping field to transform the T2s image to the PAM50 template space, informed by the shape of the gray matter.

    You can get these files by downloading data_processing-fmri-data.zip.

  2. Open a terminal and navigate to the single_subject/data/fmri/ directory:

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/fmri/