Freesurfer CRAS offset

Relyativist · December 12, 2019, 11:05am

Hi,
as a background, our team is trying to formalize nilearn issue with CRAS offsetting in .gii files.
I am trying to find out what CRAS abbreviation means. Freesurfer documentation has zero information considering CRAS orientation. Any ideas?

effigies · December 12, 2019, 5:07pm

CRAS is the translation from the central voxel to the RAS center of the image.

In some documentation it’s referred to as Pxyz_c. Some useful references in nibabel:

github.com

nipy/nibabel/blob/d1518aa71a8a80f5e7049a3509dfb49cf6b78005/nibabel/freesurfer/mghformat.py#L42


DATA_OFFSET = 284
# Note that mgh data is strictly big endian ( hence the > sign )
header_dtd = [
    ('version', '>i4'),             # 0; must be 1
    ('dims', '>i4', (4,)),          # 4; width, height, depth, nframes
    ('type', '>i4'),                # 20; data type
    ('dof', '>i4'),                 # 24; degrees of freedom
    ('goodRASFlag', '>i2'),         # 28; Mdc, Pxyz_c fields valid
    ('delta', '>f4', (3,)),         # 30; zooms (X, Y, Z)
    ('Mdc', '>f4', (3, 3)),         # 42; TRANSPOSE of direction cosine matrix
    ('Pxyz_c', '>f4', (3,)),        # 78; mm from (0, 0, 0) RAS to vol center
]
# Optional footer. Also has more stuff after this, optionally
footer_dtd = [
    ('tr', '>f4'),                  # 0; repetition time
    ('flip_angle', '>f4'),          # 4; flip angle
    ('te', '>f4'),                  # 8; echo time
    ('ti', '>f4'),                  # 12; inversion time
    ('fov', '>f4'),                 # 16; field of view (unused)
]

github.com

nipy/nibabel/blob/d1518aa71a8a80f5e7049a3509dfb49cf6b78005/nibabel/freesurfer/mghformat.py#L175-L185


def get_affine(self):
    ''' Get the affine transform from the header information.


    MGH format doesn't store the transform directly. Instead it's gleaned
    from the zooms ( delta ), direction cosines ( Mdc ), RAS centers (
    Pxyz_c ) and the dimensions.
    '''
    hdr = self._structarr
    MdcD = hdr['Mdc'].T * hdr['delta']
    vol_center = MdcD.dot(hdr['dims'][:3]) / 2
    return from_matvec(MdcD, hdr['Pxyz_c'] - vol_center)

github.com

nipy/nibabel/blob/d1518aa71a8a80f5e7049a3509dfb49cf6b78005/nibabel/freesurfer/mghformat.py#L630-L643


def _affine2header(self):
    """ Unconditionally set affine into the header """
    hdr = self._header
    shape = np.array(self._dataobj.shape[:3])


    # for more information, go through save_mgh.m in FreeSurfer dist
    voxelsize = voxel_sizes(self._affine)
    Mdc = self._affine[:3, :3] / voxelsize
    c_ras = self._affine.dot(np.hstack((shape / 2.0, [1])))[:3]


    # Assign after we've had a chance to raise exceptions
    hdr['delta'] = voxelsize
    hdr['Mdc'] = Mdc.T
    hdr['Pxyz_c'] = c_ras