trk2dictionary not working with spyder

daducci / COMMIT

Linear framework to combine tractography and tissue micro-structure estimation with diffusion MRI

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trk2dictionary not working with spyder #115

Closed simchahal1127 closed 1 year ago

simchahal1127 commented 2 years ago

Hello! I've been trying to go through the tutorial, and I'm at the point where I'm inputting trk2dictionary.run( filename_tractogram = 'demo01_fibers.tck', filename_peaks = 'peaks.nii.gz', filename_mask = 'WM.nii.gz', fiber_shift = 0.5, peaks_use_affine = True ) But it's not moving past this particular line:

- flipping axes : [ x=False, y=False, z=False ]

I was wondering if there was anything I could do to make this work?

daducci commented 2 years ago

Hi,

Could you provide us with more details in the environment you are working on? E.g. operating system, python version etc.

Also, can you open the file 'peaks.nii.gz' with any viewer, e.g. mrview? It looks like the data is corrupted.

daducci commented 2 years ago

Besides, can you please try running the script from a normal Python shell?