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daducci / COMMIT

Linear framework to combine tractography and tissue micro-structure estimation with diffusion MRI
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see an error in trk2dictionary #95

Closed mohammadhadiaarabi closed 3 years ago

mohammadhadiaarabi commented 3 years ago

Dear Developer, When I run step by step codes based on wiki page, I see an error:

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 ... ) Traceback (most recent call last): File "", line 6, in File "commit/trk2dictionary/trk2dictionary.pyx", line 27, in commit.trk2dictionary.run File "commit/trk2dictionary/trk2dictionary.pyx", line 108, in commit.trk2dictionary.run TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

I would be appreciated if you help me to fix this error. Best, Mohammad

MarioOcampo commented 3 years ago

Hello @mohammadhadiarabi ,

thanks for letting us know about this problem. I'm trying to reproduce the error. What OS and version of Python and COMMIT are you using? To obtain the version of COMMIT you can execute:

import commit
commit.__version__

Best

daducci commented 3 years ago

Also, did you install it with pip install dmri-commit or via the sources?

mohammadhadiaarabi commented 3 years ago

Thank you for rapid response. I use Ubuntu18.04 and '1.3.9.4' version of COMMIT. I installed with pip3 install dmri-commit Best, Mohammad

MarioOcampo commented 3 years ago

Could you update COMMIT? pip3 install dmri-commit --upgrade And try the code again.

mohammadhadiaarabi commented 3 years ago

I updated COMMIT, but I again see the error

MarioOcampo commented 3 years ago

In version 1.3.9.4 the error you reported happened when the tractogram was not found. In version 1.4.4, if the tractogram is not found it shows the message [ ERROR ] Tractogram file not found

Could you confirm that you have the version 1.4.4 and the tractogram file. If that is OK, could you share with us the new error message.

mohammadhadiaarabi commented 3 years ago

Dear Mario, Thank you for your help. It works now. Tnx