[Neuroimaging] Slicing images on different planes

[Satrajit Ghosh]

hi carl,

in addition to what chris said,

you may also want to consider just opening your file using neuroglancer,
which supports nifti as an input (and as long as your file is on the web
somewhere, neuroglancer will be able to open it) and has on the fly
rotation capabilities (hit the ? button to look at the keyboard shortcuts).

here is an example: https://tinyurl.com/yf2jk4af

i've intentionally created a weird orientation, you can hit z to snap back
to a default orientation. also if you click on the "source" tab on the
right, you will be able to manually change affines if you would like to.

cheers,

satra

On Sat, Mar 20, 2021 at 10:45 PM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Hi Carl,
>
> It sounds like what you want to do is to interpolate the image in a space
> that's more conveniently rotated so that image dimensions correspond to
> meaningful directions in the world and then visualize slices. The way to go
> about that is going to depend on how well the orientation is described in
> the image affine matrix.
>
> If the affine correctly describes rotations, then you can simply resample
> the image with nibabel.processing.resample_to_output() (
> https://nipy.org/nibabel/reference/nibabel.processing.html#resample-to-output).
> That will produce an image in-memory that you can work with as you show in
> your code, or save and open in another viewer.
>
> If your images don't have reliable rotation information stored (e.g.,
> img.affine[:3, :3] contains 6 zeroes), then you're going to need to find a
> rotation so that you can do something like the above. I have to imagine
> that tools exist that allow you to place axes in a 3D image and determine
> the rotation matrix, but I don't know one to suggest.
>
> Best,
> Chris
>
> ________________________________________
> From: Neuroimaging <neuroimaging-bounces+markiewicz=
> stanford.edu at python.org> on behalf of Buist, Carl R. <cbuist at ou.edu>
> Sent: Friday, March 19, 2021 3:30 PM
> To: neuroimaging at python.org
> Subject: [Neuroimaging] Slicing images on different planes
>
> Hello all,
>
> I would like to preference this question by saying that I am new to the
> world of python in general and apologize if this is a silly question and if
> my code is suboptimal. I am also not using medical data, but microCT
> scanned images of fossils, but I think that the principles for slicing the
> images are pretty similar.
>
> I have recently written a very basic code to slice a NIfTI (.nii) file
> along the major axes or some variation of those axes. Now I would like to
> slice the file along a plane that is not along one of these major axes, for
> example maybe a plane that is rotated 45 degrees off the x axis in any
> direction or something like that. My initial thought was to define a plane
> and use that in place of one of the planes I am currently displaying but am
> running into trouble.
>
> I tried to look through the archive to see if this was a problem for
> others but didn't see anything. I would really appreciate any help or if
> someone could point me in the correct direction. Below is the simple code
> that I made and attached is an image of the output.
>
> Thank you so much for your help,
> Carl
>
> def display_views(file_path):
>     image_axis = 2
>     medical_image = nib.load(file_path)
>     image = medical_image.get_fdata()
>     image = np.squeeze(image)
>     print(image.shape)
>
>     # Infer dimensions on each Cartesian axis
>     x_dim = len(image[:,0,0])
>     y_dim = len(image[0,:,0])
>     z_dim = len(image[0,0,:])
>
>     # Midpoint layers, as integers
>     x_midpoint = int(x_dim/2)
>     y_midpoint = int(y_dim/2)
>     z_midpoint = int(z_dim/2)
>
>     sagital_image = image[x_midpoint, :, :]
>     coronal_image = image[:, y_midpoint, :]
>     axial_image = image[:, :, z_midpoint]
>     axial_imagep10 = image[:, :, int(z_midpoint + 100)]
>
>     plt.figure(figsize=(20, 10))
>     plt.style.use('grayscale')
>
>     plt.subplot(141)
>     plt.imshow(np.rot90(sagital_image))
>     plt.title('Sagital Plane')
>     plt.axis('off')
>
>     plt.subplot(142)
>     plt.imshow(np.rot90(coronal_image))
>     plt.title('Coronal Plane')
>     plt.axis('off')
>
>     plt.subplot(143)
>     plt.imshow(np.rot90(axial_image))
>     plt.title('Axial Plane')
>     plt.axis('off')
>
>     plt.subplot(144)
>     plt.imshow(np.rot90(axial_imagep10))
>     plt.title('Axial Plane moved')
>     plt.axis('off')
>
>     plt.show()
>
> #fpath = sys.argv[1]
> fpath =
> '/content/drive/MyDrive/3D_Forams/Foram_NH1108sit_gdr_7_1__IR_rec480-1180_testcrop.nii'
>
> display_views(fpath)
>
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