yunyunjin
commented
3 months ago Open yunyunjin opened 3 months ago
yunyunjin
commented
3 months ago 
GaoxingZheng
commented
3 months ago Hi, the information you showed in the panel is not the key error information, can you give more details? Such as the WMA 'kill' error when doing wm_cluster_from_atlas.py step. I guess the error will be earlier than the information above.
yunyunjin
commented
3 months ago Thank you for your quick response. Here is the top part of the error. The old WMA error generated log.txt, but this time no such log file was created. So I'm not sure which part is the error.
<wm_separate_clusters_by_hemisphere.py> Done!!!
Importing whitematteranalysis package.
<wm_append_clusters_to_anatomical_tracts.py> 41 mrml files are detected.
<wm_append_clusters_to_anatomical_tracts.py> Output directory /usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/AnatomicalTracts/ does not exist, creating it.
<wm_append_clusters_to_anatomical_tracts.py> hemispheric tracts (left and right):
* 1 - T_AF
* 2 - T_CB
* 3 - T_EmC
* 4 - T_ILF
* 5 - T_IOFF
* 6 - T_MdLF
* 7 - T_SLF-I
* 8 - T_SLF-II
* 9 - T_SLF-III
* 10 - T_UF
* 11 - T_CPC
* 12 - T_ICP
* 13 - T_Intra-CBLM-I&P
* 14 - T_Intra-CBLM-PaT
* 15 - T_EC
* 16 - T_CR-F
* 17 - T_CR-P
* 18 - T_CST
* 19 - T_PLIC
* 20 - T_SF
* 21 - T_SO
* 22 - T_SP
* 23 - T_TF
* 24 - T_TO
* 25 - T_TP
* 26 - T_Sup-F
* 27 - T_Sup-FP
* 28 - T_Sup-O
* 29 - T_Sup-OT
* 30 - T_Sup-P
* 31 - T_Sup-PO
* 32 - T_Sup-PT
* 33 - T_Sup-T
<wm_append_clusters_to_anatomical_tracts.py> commissural tracts:
* 34 - T_CC1
* 35 - T_CC2
* 36 - T_CC3
* 37 - T_CC4
* 38 - T_CC5
* 39 - T_CC6
* 40 - T_CC7
* 41 - T_MCP
<wm_append_clusters_to_anatomical_tracts.py> Appended tracts can be found at /usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/AnatomicalTracts
<wm_append_clusters_to_anatomical_tracts.py> A total of 74 tracts
Importing whitematteranalysis package.
<wm_quality_control_tractography.py> Starting...
<wm_quality_control_tractography.py> Found 74 subjects in input directory /usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/AnatomicalTracts/
<wm_quality_control_tractography.py> Testing all files for quality control (computing fiber length measurements and rendering to make sure header and gradient orientations are ok).
<wm_quality_control_tractography.py> See the README.txt file in the output directory for more overview information.
Subject 1 / 74 ID: T_AF_left
2024-07-18 01:27:03.724 ( 0.550s) [ 7F90B9FC1740]vtkXMLUnstructuredDataR:404 WARN| vtkXMLPolyDataReader (0x26f2060): No Points element available in first piece found in file. Reading file may fail.
<filter.py> No fibers found in input polydata.
<render.py> Saving rendered views to disk: /usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
Multiple views for individual subject
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
tract_QC_T_AF_left/view_left_T_AF_left.jpg
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left/view_multiple_T_AF_left.html
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
tract_QC_T_AF_left/view_right_T_AF_left.jpg
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left/view_multiple_T_AF_left.html
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
tract_QC_T_AF_left/view_inf_T_AF_left.jpg
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left/view_multiple_T_AF_left.html
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
tract_QC_T_AF_left/view_sup_T_AF_left.jpg
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left/view_multiple_T_AF_left.html
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
tract_QC_T_AF_left/view_ant_T_AF_left.jpg
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left/view_multiple_T_AF_left.html
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left
tract_QC_T_AF_left/view_post_T_AF_left.jpg
/usr/local/MATLAB/R2019b/toolbox/UFA_toolbox/WMA_clustering_SWM/QC/AnatomicalTracts/tract_QC_T_AF_left/view_multiple_T_AF_left.html
<filter.py> No fibers found in input polydata.
Subject 2 / 74 ID: T_AF_rightHi, there doesn't seem to be an error message in there, just some warnings, the error message should be something like error. Some minor problems with your vtk might be due to vtk configuration issues, but this doesn't seem to have much impact, at most on the visualisation rendering. BTW, no fibers in the input data is because we only clustered superficial u-fibers, and 74 brain regions are both deep and superficial fibers, so of course there are no fibers in deep brain regions. In the last two days I have updated the pipeline, and the clustering and quantitative analysis of the whole white matter fiber tracts have been put into the toolbox, and there will be a word document giving instructions for the update.
---- Replied Message ---- | From | @.> | | Date | 07/18/2024 10:13 | | To | GaoxingZheng/UFA_toolbox @.> | | Cc | GaoxingZheng @.>, Comment @.> | | Subject | Re: [GaoxingZheng/UFA_toolbox] No fibers found in input polydata & No Points element available in U-fiber clustering (Issue #3) |
Thank you for your quick response. Here is the top part of the error.
yunyunjin
commented
3 months ago Thank you so much for the update and your continued support. I am currently using the updated toolbox, but I encountered the same error. It seems similar to this issue https://github.com/Slicer/Slicer/issues/6447. The usual solution is to update the version, but as I understand, the UFA toolbox requires using 3D Slicer version 4.8.1. Unfortunately, modifying the VTK source seems beyond my capabilities.
So far, I have only tested this with one subject. However, it’s possible that this error might not occur with others, so I will proceed with additional subjects to see if the issue persists. Thank you once again for your kindly comment.
GaoxingZheng
commented
3 months ago Thank you so much for the update and your continued support. I am currently using the updated toolbox, but I encountered the same error. It seems similar to this issue Slicer/Slicer#6447. The usual solution is to update the version, but as I understand, the UFA toolbox requires using 3D Slicer version 4.8.1. Unfortunately, modifying the VTK source seems beyond my capabilities.
So far, I have only tested this with one subject. However, it’s possible that this error might not occur with others, so I will proceed with additional subjects to see if the issue persists. Thank you once again for your kindly comment.
Hi, can you send the WMA_clustering_SWM folder as a zip file to my email (zheng_gao_xing@163.com)? You can delete some large files and compress the remaining files to me. I'll check what's wrong with your code.
Hello,
I have checked the 'WMA package bug fix' you provided earlier. Thanks to your help, I was able to resolve the initial bug and generate new outputs. However, I have now encountered another issue while using the U-fiber clustering feature in the UFA toolbox. The process fails with errors indicating that no fibers are found in the input polydata and that there are no points available in the input files.
Errors:
Additional Steps Taken: I followed the instructions to install Slicer Extensions:
Opened 3D Slicer and tried to search for the SlicerDMRI Extension. When the search function didn't work, I installed SlicerDMRI from a file. Initially, the installation didn't seem complete because the SlicerDMRI icon was missing (it should appear as a puzzle piece on a blue background). I clicked update, and the installation completed successfully with the correct SlicerDMRI module icon. I was then prompted to install an additional extension, UKFTractography. I installed it, but I'm not sure if it installed correctly. Could the issue be related to the incomplete installation of the UKFTractography extension? Any guidance or fixes to address this issue would be greatly appreciated.
full version:
Thank you.