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SlicerDMRI / SupWMA

[MedIA 2023] "Superficial White Matter Analysis: An Efficient Point-cloud-based Deep Learning Framework with Supervised Contrastive Learning for Consistent Tractography Parcellation across Populations and dMRI Acquisitions", Medical Image Analysis
https://supwma.github.io
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ask for help #3

Open houxiaolinzhengdan opened 2 years ago

houxiaolinzhengdan commented 2 years ago

Dear Zhang, I am Hou Xiaolin, a neurosurgeon from the Affiliated Hospital of Chengdu University of Traditional Chinese Medicine. I was lucky to see your Supwma study. I used your Git code. According to the instructions, there will be mistakes, I would like to ask you how to solve this problem, thank you. Is this a problem with the 3dslicer version? 123456

tengfeixue-victor commented 2 years ago

Hi Xiaolin,

Thanks for reporting this! Sorry for the inconvenience. It's not your problem. I fixed this bug. You can git clone the updated code and give a try again. Please let us know if you have any questions.

Thanks, Tengfei

houxiaolinzhengdan commented 2 years ago

thank you ,but i still have an other question.Statistical analysis of fiber bundles was not available， Is this a problem with the 3dslicer version or a bug Screenshot from 2022-05-02 23-46-45 ?

zhangfanmark commented 2 years ago

Hi @houxiaolinzhengdan

Please try:

wm_diffusion_measurements.py inputfolder outputcsv “Path_to_Sicer_executable/Slicer --launch FiberTractMeasurements”

In this way, the program will be able to load the related libraries. Note: please keep the quotes.

Regards, Fan

houxiaolinzhengdan commented 2 years ago

Sorry to bother you again, I have followed your instructions, but there is still a problem. FiberTractMeasurements cannot be found, but this file actually exist in 3DSLicer (it was available after version 4.11). I have changed several versions of 3Dslicer, but it still cannot be solved the problem. Could you please take a look at the problem, thank you very much.

houxiaolinzhengdan commented 2 years ago

Sorry to bother you again, I have followed your instructions, but there is still a problem. FiberTractMeasurements cannot be found, but this file actually exist in 3DSLicer (it was available after version 4.11). I have changed several versions of 3Dslicer, but it still cannot be solved the problem. Could you please take a look at the problem, thank you very much! Screenshot from 2022-05-04 09-55-39

zhangfanmark commented 2 years ago

Hi,

Slicer 4.10.2 should work (Slicer 4.11 should also work). Please make sure that you have installed SlicerDMRI: http://dmri.slicer.org/download/

Regards, Fan

houxiaolinzhengdan commented 2 years ago

i have tried the 3Dslicer 4.10.2 and install the SlicerDMRI, but it still not work! Screenshot from 2022-05-04 10-25-27 Screenshot from 2022-05-04 10-25-48

zhangfanmark commented 2 years ago

Not sure if this is true, but it seems the quotes are not in English. Can you try to change your keyboard input?

houxiaolinzhengdan commented 2 years ago

i have solve the problem. thank you very much! but i have another question, When I imported the segmented nerve fibers into 3Dslicer, the spatial position was incorrect, Is there a solution for the problem? Screenshot from 2022-05-04 11-22-06

tengfeixue-victor commented 2 years ago

Hi, it seems you need to transfer the parcellation results back to the subject space. Please refer to the answer here to if it helps.

If you have any questions, please feel free to let us know.

Thanks, Tengfei