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Hi gang,

I hope you're enjoying the last stretch of summer!

I am writing a python code that reads NIfTI images, changes their coordinate system into LAS (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm), and then saves the corrected NIfTI mage. 

The function that corrects the coordinate system is copied below. I am not sure if I am changing the affine transform (from the MRI space to the scanner space) correctly. 

For instance, to go from LPS to LAS, I should flip the image in 2nd dimension. The piece that I'm not sure about is if I should negate the 2nd column of the affine matrix or if the affine correction is more complicated:

image = np.flip(image, 1)
affine[:, 1] = - affine[:, 1]

I would really really appreciate any help here! I'm stuck :D 

Cheers,

Arman

-----------------------------------------------------------------

def correct_coordinates(image, affine, coords):
    """
    This function re-orients the MRI volume into the standard radiology system, i.e. ('L','A','S'),
    and also corrects the affine transform for the volume (from the MRI volume space to the scanner space).
    Inputs:
        - image: MRI volume
        - affine: affine transform for the MRI volume 
            (e.g. [[-5, 0, 0, 1]
                   [0, -5.2, 7.8  1.6]
                   [0, 6.9, 5.9, -7.7]
                   [0,  0,  0,  1]]
        - coords: the coordinate system of the MRI volume (e.g. ('L', 'P', 'S')
        
    Outputs:
        - image: corrected MRI volume in the standard radiology coordinate system: ('L', 'A', 'S')
        - affine: corrected affine transform (from MRI volume space to the scanner space).
    """
    if coords == ('L', 'A', 'S'):
        return image, affine

    if coords == ('R', 'A', 'S'):
        image = np.flip(image, 0)
        affine[:, 0] = - affine[:, 0]
        return image, affine

    if coords == ('L', 'P', 'S'):
        image = np.flip(image, 1)
        affine[:, 1] = - affine[:, 1]
        # print('func coords: ', coords)
        # print('func corr coords: ', nib.aff2axcodes(affine))
        # print('function affine: \n', affine)
        return image, affine

    if coords == ('L', 'S', 'A'):
        image = np.swapaxes(image, 1, 2)
        affine[:, [1, 2]] = affine[:, [2, 1]]
        return image, affine

    if coords == ('L', 'I', 'A'):
        # L,I,A --> L,A,I
        image = np.swapaxes(image, 1, 2)
        affine[:, [1, 2]] = affine[:, [2, 1]]
        # L,A,I --> L,A,S
        image = np.flip(image, 2)
        affine[:, 2] = - affine[:, 2]
        return image, affine
    if coords == ('L', 'P', 'S'):
        image = np.flip(image, 1)
        affine[:, 1] = - affine[:, 1]
        return image, affine

    if coords == ('L', 'I', 'P'):
        # L,I,P --> L,I,A
        image = np.flip(image,2)
        affine[:, 2] = - affine[:, 2]
        # L,I,A --> L,A,I
        image = np.swapaxes(image, 1, 2)
        affine[:, [1, 2]] = affine[:, [2, 1]]
        # L,A,I --> L,A,S
        image = np.flip(image, 2)
        affine[:, 2] = - affine[:, 2]
        return image, affine

    if coords == ('P', 'I', 'R'):
        # P,I,R --> A,I,R
        image = np.flip(image, 0)
        affine[:, 0] = - affine[:, 0]
        # A,I,R --> A,S,R
        image = np.flip(image, 1)
        affine[:, 1] = - affine[:, 1]
        # A,S,R --> A,S,L
        image = np.flip(image, 2)
        affine[:, 2] = - affine[:, 2]
        # A,S,L --> L,A,S
        image = np.moveaxis(image, [0, 1, 2], [1, 2, 0])
        affine[:, [0, 1, 2]] = affine[:, [1, 2, 0]]
        return image, affine

    raise Exception('coords not identified: please go to correct_coordinates function '
                    'and define the coordinate system.')

---

Arman Avesta, MD
PhD student in the combined radiology residency & PhD training program
Yale School of Medicine & Yale Graduate School of Arts and Sciences

195 Church St 6^th Floor, New Haven, CT 06510 

arman.avesta@yale.edu
medicine.yale.edu/profile/arman_avesta 

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