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fumiado opened this issue Mar 8, 2023 · 19 comments
Open

Error: python setup.py bdist_wheel #122

fumiado opened this issue Mar 8, 2023 · 19 comments

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@fumiado
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fumiado commented Mar 8, 2023

Hi, while I am trying to install whitematteranalysis with 'pip install git+https://github.com/SlicerDMRI/whitematteranalysis.git', there was an error message below:
Anaconda Prompt (miniconda3).txt
Would anyone tell me how to solve this error?
I am using Windoows, Python 3.10, Miniconda 3.

Thank you,
@zhangfanmark
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Hi @fumiado ,

WMA is well tested on MacOS and Linux but not windows. We will look into this. Meanwhile, if you have a Mac or linux machine available, please try them, or if you want to install a VM temporarily.

Thanks,
Fan

@fumiado
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fumiado commented Mar 15, 2023

Hi Fan,

Thank you so much for your comment on my issue. I tried WMA installation in my Linux PC again, then succeeded!

I would ask you another question, is this whitematteranalysis system able to use in pediatric datasets? I read your article on Neuroimage published in 2018, and found your study including very young chindren. What I am going to do is to analys DTI tractography in school age patients. I would be happy if you don't mind my asking and would tell me any advice on this topic.

Sincerely,
Fumi

@zhangfanmark
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Hi Fumi,

For school age patients, you should be able to run WMA directly, without any additional processing. Basically, you will need to run UKF tractography first, which is available in 3D Slicer via SlicerDMRI. Then, you can use the computed tractography data as input into WMA to extract the fiber tracts.

Regards,
Fan

@fumiado
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fumiado commented Mar 15, 2023

Hi Fan,

I appreciate to your quick reply ! OK, now I know I can continue to do this analysis using WMA in my study.

As to UKFTractography, I am using UKF Tractography Titorial PDF by Pegah Kahali, and did not understand how to create the 'Input Label Map' on Slicer 5.2.2. For seeding, though I could have created Segmentation_Labelmap with Segment editor module, that segmented label map is not proper for whole brain tractography I guess.
Any advice woukd be appreciated!

Thank you,
Fumi

@zhangfanmark
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Hi, in the UKF tutorial, there are slides about how to create a brain mask using the Diffusion Brain Masking module. This mask should be used as input label map.

Regards
Fan

@fumiado
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fumiado commented Mar 15, 2023

Ah, mask can be used as label map! Thank you for your kind support! I will try again.

Fumi

@fumiado
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fumiado commented Mar 16, 2023

Hi Fan,

While I continued WMA woking on WMA tutorial (https://github.com/SlicerDMRI/whitematteranalysis/blob/master/doc/subject-specific-tractography-parcellation.md) with tutorial data, I couldn't get any CSV file at "8. Fiber tract diffusion measurements". From the tutorial command, I changed the location of SlicerDMRI in my PC. I attached the error terminal.
Error_fibertractdiffusionmeasurement.txt

I am using Slicer 5.2.2, because some error in seeding process before ver 5.1. I couldn' t find any "/cli-modules/FiberTractMeasurements" folder in Slicer5.2, and I guess this may be the reason for this error? If you have any solution about this, would you please let me know?

Thank you,
Fumi

@fumiado
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fumiado commented Mar 16, 2023

Hi, I need to apologize for the issue ahead, I found the "/cli-modules/FiberTractMeasurements" folder in Slicer5.2 as well as in command. So, now I still have more question on why that command didn't work well.

Thank you,
Fumi

@ljod
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ljod commented Mar 22, 2023 via email

@fumiado
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fumiado commented Mar 23, 2023

Hi Lauren, thanks so much for your reply. Actually I posted the similar question on Slicer Community (https://discourse.slicer.org/t/no-csv-file-in-diffusionmessurements-folder-in-wma/28439/3) as well, and I've got an anser from Fan. He suggested to call the fiber measurement module at that moment, and I tried that command which was failed again.

Command: wm_diffusion_measurements.py ./FiberClustering/SeparatedClusters/tracts_commissural/ ./DiffusionMeasurements/commissural_clusters.csv “/home/brain/Downloads/Slicer-5.2.2-linux-amd64/Slicer --launch FiberTractMeasurements”

Error message: wm_diffusion_measurements.py ./FiberClustering/SeparatedClusters/tracts_commissural/ ./DiffusionMeasurements/commissural_clusters.csv “/home/brain/Downloads/Slicer-5.2.2-linux-amd64/Slicer --launch FiberTractMeasurements”

I succeeded in the "7. Identification of anatomical tracts" step, and could get all date.
This error happens to both input tutorial data and my own data.
I will appreciate to any suggestion for this problem.
Thank you,
Fumi

@fumiado
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fumiado commented Mar 23, 2023

Sorry, the above error message was not correct.
Error message: Importing whitematteranalysis package.
usage: wm_diffusion_measurements.py [-h] [-v] inputDirectory outputCSV Slicer
wm_diffusion_measurements.py: error: unrecognized arguments: --launch FiberTractMeasurements”

@ljod
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ljod commented Mar 23, 2023 via email

@fumiado
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fumiado commented Mar 23, 2023

I tried first the slicer command written in the WMA tutorial "8. Fiber tract diffusion measurements" as below:

Command: wm_diffusion_measurements.py ./FiberClustering/SeparatedClusters/tracts_commissural/ ./DiffusionMeasurements/commissural_clusters.csv /home/brain/Downloads/Slicer-5.2.2-linux-amd64/NA-MIC/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/FiberTractMeasurements

Error message: /home/brain/Downloads/Slicer-5.2.2-linux-amd64/NA-MIC/Extensions-31382/SlicerDMRI/lib/Slicer-5.2/cli-modules/FiberTractMeasurements: error while loading shared libraries: libSlicerBaseLogic.so: cannot open shared object file: No such file or directory
<wm_diffusion_measurements> Measurements done at: ./DiffusionMeasurements/commissural_clusters.csv

The “DiffusionMeasurements” folder was created without any CSV files.
I think the location for the FiberTractMeasurements is correct, so didn't understand why cannot open the file as in the error message...

I appreciate to your help,
Fumi

@zhangfanmark
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Hi Fumi,

This should be working but I am not sure what is going wrong here.

Please try our master script: wm_apply_ORG_atlas_to_subject.sh, which allows you to run all steps in one command, rather than running each command individually.

Please note -m should be with the quotes, “/home/brain/Downloads/Slicer-5.2.2-linux-amd64/Slicer --launch FiberTractMeasurements”.

If there is still an issue, please try an older version of Slicer v4.10.

If these all do not work, I am happy to have a zoom meeting and take a look at the errors with you together.

Regards,
Fan

@fumiado
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fumiado commented Mar 25, 2023

Hi Fan, thank you for your kind suggestion, but I still have problem. Because I am not sure on ShellScript, I need to ask how to use "wm_apply_ORG_atlas_to_subject.sh". Do I need make up shell acripts using Compulsory arguments and Optional arguments which I need ? I tried this some times, but it didn't work. I feel so sorry to ask such a basic question to you, but can you give me an example?

@zhangfanmark
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@fumiado The bdist_wheel issue happened on Widows should have been fixed. Please let us know if it works for you. Then we can resolve the issue. Thanks.

Regards,
Fan

@fumiado
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fumiado commented Apr 15, 2023

Hi Fan, thank you for letting me know about the Windows fixation, I could installed WMA using miniconda without any problem on my Windows!

Well, I'm still working on how to get CSV files for Fiber tract diffusion measurements.
I could not use master script well.
Then I tried Slicer v4.10.0-2 for Linux and Windows. Linux Slicers v4.10 could not restart right after installing Exchange of SlicerDMRI and SlicerWMA. I could not find out SlicerWMA in Exchange Manager for Windows Slicers v4.10.

Is there any solution for this issue? If you have any idea for this, please tell me how to do!

Fumi

@jhlegarreta
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The issues when computing the FiberTractMeasurements module's bundle measurements and getting the corresponding CSV data file written on Linux were solved using the call proposed in the Slicer discourse thread (the key being the entire argument to the -m option).

Unfortunately, I cannot comment on the Python setup error on Windows.

@fumiado
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fumiado commented Jul 12, 2023

Thank you @jhlegarreta for commenting on this issue! Now I am trying again!

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@ljod @jhlegarreta @zhangfanmark @fumiado