\(\newcommand{L}[1]{\| #1 \|}\newcommand{VL}[1]{\L{ \vec{#1} }}\newcommand{R}[1]{\operatorname{Re}\,(#1)}\newcommand{I}[1]{\operatorname{Im}\, (#1)}\)

Cross-subject registration

Logistics

• problems from projects;

Teaching

• Making and saving new images in nibabel;

• SPM coregistration:

  • copy the structural:

    cp ds107_sub012_highres.nii a_structural.nii
    

  • create the mean of the functional image:

    >>> import nibabel as nib
    >>> img = nib.load('ds107_sub012_t1r2.nii')
    >>> mean_vol = img.get_data().mean(axis=-1)
    >>> mean_img = nib.Nifti1Image(mean_vol, img.affine, img.header)
    >>> nib.save(mean_img, 'mean_functional.nii')
    

  • run coregistration in SPM.

• running cross-subject normalizations in SPM;

• making a distortion field in SPM;

• applying the SPM distortion field;

  • Removing length 1 axes with numpy.squeeze;
  • numpy.tranpose for swapping axes;
  • Making coordinate arrays with meshgrid;
  • General resampling between images with scipy.ndimage.map_coordinates;
  • Applying deformations exercise.

Reading and homework

Working on projects.