DOSMA
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ad12
An AI-powered open-source medical image analysis toolbox
Starting a pull request while working on this to get feedback. A few things are done differently than other models. - Currently loading model + weights from .h5 file (vs....
Looks like ITK now has a builtin pip installable version of elastix (https://discourse.itk.org/t/itkelastix-0-16-0-has-been-released/5736). It might be worth looking into incoporating. It would: 1. Simplify installation. 2. Enable more flexible use...
**Describe the bug** A clear and concise description of what the bug is. https://github.com/ad12/DOSMA/blob/bd5efecbb944263c9a5d7853f154d9071c72ba62/dosma/scan_sequences/mri/mapss.py#L225-L232 The above section of code shows that the tissue class is required for the T2 generation...
I want to include in dosma in a docker container. All works fine, but the container must be run as root because dosma wants to write to a logfile which...
The `group_by` argument of `DicomReader` currently defaults to `EchoNumbers`, which is not commonly present in DICOM files. Typically, I would only load one DICOM study and not use grouping at...
For some DICOM datasets I would like to order the slices based on multiple tags. For example, in a dataset with a `TemporalPositionIdentifier` present, I would like to sort by...
**Describe the bug** When using `dm.register` sometimes an error is thrown indicating that the transform file is not found: ``` FileNotFoundError: No such file or directory '['/dataNAS/people/jdemarre/repeat_3T7T/Repeatability/results_April-04-2022/repeat001/3T/9582/elastix_reg_2/moving-0/TransformParameters.0.txt']' for output 'transform'...
Importing tensorflow can take a lot of time. To solve this, we can make the tensorflow imports lazy