whitematteranalysis Error: python setup.py bdist

Error: python setup.py bdist_wheel

Open fumiado opened this issue 1 year ago • 19 comments

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,

Mar 08 '23 04:03 fumiado

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

Mar 15 '23 02:03 zhangfanmark

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

Mar 15 '23 03:03 fumiado

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

Mar 15 '23 04:03 zhangfanmark

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

Mar 15 '23 06:03 fumiado

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

Mar 15 '23 06:03 zhangfanmark

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

Fumi

Mar 15 '23 06:03 fumiado

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

Mar 16 '23 01:03 fumiado

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

Mar 16 '23 02:03 fumiado

Hi Fumi if you are still working on this please provide the command you ran and the error message that resulted. You can also post to https://discourse.slicer.org/ for general Slicer and CLI questions.

Lauren J. O’Donnell, Ph.D. Associate Professor, Harvard Medical School

From: fumiado @.> Sent: Wednesday, March 15, 2023 10:59 PM To: SlicerDMRI/whitematteranalysis @.> Cc: Subscribed @.***> Subject: Re: [SlicerDMRI/whitematteranalysis] Error: python setup.py bdist_wheel (Issue #122)

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Thank you, Fumi

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Mar 22 '23 17:03 ljod

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

Mar 23 '23 00:03 fumiado

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”

Mar 23 '23 01:03 fumiado

It looks like your command line formatting of the slicer command is not working. Does it work if you just give only the path to slicer without the launch measurement part? It seems the python script should handle that part once it knows where slicer is located.

Lauren J. O’Donnell, Ph.D. Associate Professor, Harvard Medical School 399 Revolution Drive, Suite 1180 Somerville, MA 02145 @.***

From: fumiado @.> Sent: Wednesday, March 22, 2023 9:02 PM To: SlicerDMRI/whitematteranalysis @.> Cc: O'Donnell, Lauren J., Ph.D. @.>; Comment @.> Subject: Re: [SlicerDMRI/whitematteranalysis] Error: python setup.py bdist_wheel (Issue #122)

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Mar 23 '23 10:03 ljod

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

Mar 23 '23 11:03 fumiado

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

Mar 23 '23 12:03 zhangfanmark

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?

Mar 25 '23 07:03 fumiado

@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

Apr 07 '23 11:04 zhangfanmark

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

Apr 15 '23 07:04 fumiado

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.

Jul 06 '23 14:07 jhlegarreta

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

Jul 12 '23 01:07 fumiado

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Error: python setup.py bdist_wheel

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