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sjames40

mridata-recon's Issues

2D or 3D FSE?

Hi,

on your README.md page, it points to an mridata.org dataset for which the recon_fse_2d.py script should work.
However, that link redirects to

http://mridata.org/list?project=Stanford%20Fullysampled%203D%20FSE%20Knees

Which is the 3D case as you can see.. So my next question is... assuming that there is a typo in the link. Do you also have a script to convert the 3D-FSE .h5 data to an image?

Also, why isnt there an easy setup.py script to install these pieces of code as a library that can be imported?

-p PNG not working properly

imageio error:
ValueError: Could not find a format to write the specified file in mode 'i'

In Windows:

FSE phase correction...
Transforming k-space data to image domain...
Writing files...
Writing example png...
Traceback (most recent call last):
  File "D:\projects\mridata-recon-master\recon_2d_fse.py", line 265, in <module>
    file_png=args.png, verbose=args.verbose)
  File "D:\projects\mridata-recon-master\recon_2d_fse.py", line 247, in dataset_to_cfl
    imageio.imwrite(file_png, image_out.astype(np.uint8))
  File "C:\Program Files\Python35\lib\site-packages\imageio\core\functions.py", line 244, in imwrite
    writer = get_writer(uri, format, 'i', **kwargs)
  File "C:\Program Files\Python35\lib\site-packages\imageio\core\functions.py", line 170, in get_writer
    'in mode %r' % mode)
ValueError: Could not find a format to write the specified file in mode 'i'

In Linux:

Transforming k-space data to image domain...
Writing files...
Writing example png...
Traceback (most recent call last):
File "/Data2/sruser/projects/mridata-recon-master/recon_2d_fse.py", line 265, in <module>
file_png=args.png, verbose=args.verbose)
File "/Data2/sruser/projects/mridata-recon-master/recon_2d_fse.py", line 247, in dataset_to_cfl
imageio.imwrite(file_png, image_out.astype(np.uint8))
File "/Data2/sruser/PycharmProjects/superres/venv/lib/python3.5/site-packages/imageio/core/functions.py", line 244, in imwrite
writer = get_writer(uri, format, 'i', **kwargs)
File "/Data2/sruser/PycharmProjects/superres/venv/lib/python3.5/site-packages/imageio/core/functions.py", line 170, in get_writer
'in mode %r' % mode)
ValueError: Could not find a format to write the specified file in mode 'i'

any ideas?

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