Do these models take in DICOM files?

[lesliewubbel]

Please use MONAI's Discussions tab
For questions relating to MONAI usage, please do not create an issue.

Instead, use MONAI's GitHub Discussions tab. This can be found next to Issues and Pull Requests along the top of our repository.

Greetings Monai team,

I read awhile ago that Monai doesn't currently support DICOM files is that true? if so how could I help develop a pipeline line
I am working on some code and small project to convert DICOM to .nii which c++ code already exist to support that but I mean more specifically for data pipeline for monai. I am really impressed by the project! thank you!

Leslie

[Nic-Ma]

Hi @Gresliebear ,

Thanks for your interest here.
MONAI can load DICOM images from v0.4, you can check this tutorial for more details:
https://github.com/Project-MONAI/tutorials/blob/master/modules/load_medical_images.ipynb

Thanks.

[oscarramirezs]

Hi Nic-Ma

thank you for the réponse,

im trying to use dice files but the matrix en dicom are 512512deep and nifty are deep512512, how can I figure-out a solution for this issue?

Oscar

[lesliewubbel]

Thank you Nic!

[Nic-Ma]

Hi Nic-Ma

thank you for the réponse,

im trying to use dice files but the matrix en dicom are 512_512_deep and nifty are deep_512_512, how can I figure-out a solution for this issue?

Oscar

Hi @ericspod ,

I am not very familiar with DICOM details, could you please help share some comments on this question?

Thanks in advance.

[lesliewubbel]

@Nic-Ma

Hes talking about when a DICOM file or a stack of DICOM files created into lets say a python object we can pull its metadata for the shape

DICOM_object.shape
prints out (512,512, 200) which means that each dicom file or 'image' or 'slice' has a height and width of 512 pixels. The 200 is the number of slices or how "deep" the whole stack. so logical we know (x,y,z) but nifty files orientation are flipped (z,x,y)

https://www.semanticscholar.org/paper/The-first-step-for-neuroimaging-data-analysis%3A-to-Li-Morgan/744629069861e2a6af9f793268ce8240181b54d1/figure/0
Nifty files flips to (200, 512, 512) what happened is that the spatial orientation changed because DICOM files are read by radiologist who used left-handed view in their spatial orientation. When neurologists read right hand in their spatial orientation therefore nitfy files are just the inverse of 3D DICOM files. The reason being nii files were created originally for neurologist looking at MRI or fMRI data.

to convert DICOM to nifty use the dicom2nitfi package https://github.com/icometrix/dicom2nifti

[rijobro]

There is also np.moveaxis and MONAI's Flip should you want to reorder dimensions and their directions, respectively.

[ericspod]

@Nic-Ma , @Gresliebear 's description is what I've found with Nifti coordinate spaces and the RAS/LAS orientations. DICOM files generally represent the image orientation as two vectors in a common scanner space. The rotation between Nifti-space and that common space is pi/2 around the Z axis as his figure shows.

[lesliewubbel]

@ericspod thank you for the information! I am self-taught so the terminology can be confusing if something is wrong in my description please point it out.

[ericspod]

I've always just been informal about the DICOM orientations, X is to the left, Y is to the back, Z is to the head.

[Nic-Ma]

@ericspod , thanks for your information, so what's the next steps? Should we modify anything?

Thanks.

[aylward]

There is a nice explanation of DICOM vs "Laboratory/Display" orientation and Neurosurgery vs Radiological image display at https://itk.org/Wiki/Proposals:Orientation#Some_notes_on_the_DICOM_convention_and_current_ITK_usage

…

On Mon, Feb 15, 2021 at 8:09 PM Eric Kerfoot ***@***.***> wrote: I've always just been informal about the DICOM orientations, X is to the left, Y is to the back, Z is to the head. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1580 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACEJL7SE7PWVKO232WMN3LS7HAS7ANCNFSM4XREKNBA> .

-- Stephen R. Aylward, Ph.D. Senior Director of Strategic Initiatives --- Kitware: *Delivering innovative, open source, scientific software.*

[oscarramirezs]

it is possible to add to the monai.transforms a fonction such => image= torch.transpose(image, 0, 1)??