Error when run sulcalpitsExtraction

[HusBunia]

Dear BrainVisa expeerts :

I'm still somewhat confused about some of the data formats, so my questions may seem a bit naive, please forgive me. I have run the sulcalpitextraction from axon-process. The command I used is
axon-runprocess SulcalPitsExtraction /casa/home/f01200624V005/surf/lh.white.gii left /casa/home/f01200624V005/surf/lh.white_pole_cingular.gii 0.03 1.5 20.0 236.18 50.0 91312.2 /casa/home/f01200624V005/surf/lh.white_DPF.gii /casa/home/f01200624V005/lh.white_pits.gii /casa/home/f01200624V005/surf/lh.white_noisy_pits.gii /casa/home/f01200624V005/surf/lh.white_ridges.gii /casa/home/f01200624V005/surf/lh.white_basins.gii

lh.white.gii is converted by mris_convert from a freesurfer recon-all output.

But I fouod it always return errors like below:

`Initializing brainvisa... (takes a while)...

Process Sulcal Pits Extraction started on 2023/05/19 23:07

Computing Vertex Voronoi
-percent polygon with obtuse angle  20.59381214447579

computing DPF

Computing Laplacian
Computing mesh weights
-edge length threshold needed for  0  values =  0.0  %
-number of Nan in weights:  0  =  0.0  %
-number of Negative values in weights:  32862  =  4.221585040620327  %
-nb Nan in L :  0
-nb Inf in L :  0

DPF done

Computing the Fiedler geodesic length and surface area

Computing Laplacian
Computing mesh weights
-edge length threshold needed for  0  values =  0.0  %
-number of Nan in weights:  0  =  0.0  %
-number of Negative values in weights:  32862  =  4.221585040620327  %
-nb Nan in L :  0
-nb Inf in L :  0

Computing GEODESIC distance between the max and min
i: 778426number of the points in the path = 503, length of the path = 225.546

Computing the watershed with distance and ridge criteria for basins merging

i: 778426

ERROR: in Sulcal Pits Extraction 1 **
TypeError: 'float' object cannot be interpreted as an integer
**

---

**TypeError**
TypeError: 'float' object cannot be interpreted as an integer

Process Sulcal Pits Extraction finished on 2023/05/19 23:09 (1 minutes 48
seconds)

Traceback (most recent call last):
File "/casa/install/bin/axon-runprocess", line 4, in
run_module('brainvisa.axon.runprocess')
File "/usr/lib/python3.10/runpy.py", line 227, in run_module
return _run_code(code, {}, init_globals, run_name, mod_spec)
File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/casa/install/python/brainvisa/axon/runprocess.py", line 512, in
run_process_with_distribution(
File "/casa/install/python/brainvisa/axon/runprocess.py", line 270, in run_process_with_distribution
brainvisa.processes.defaultContext().runProcess(process)
File "/casa/install/python/brainvisa/processes.py", line 3120, in runProcess
six.reraise(type(e[0]), e[0], e[1])
File "/usr/lib/python3/dist-packages/six.py", line 719, in reraise
raise value
File "/casa/install/python/brainvisa/processes.py", line 3412, in _processExecution
result = process.execution(self)
File "/casa/install/brainvisa/toolboxes/cortical_surface/processes/anatomy/SulcalPitsExtraction.py", line 151, in execution
labels_1, pitsKept_1, pitsRemoved_1, ridgePoints, parent_1 = watershed.watershed(mesh, vert_voronoi, dpf[0], mask, thresh_dist, self.thresh_ridge)
File "/casa/install/python/brainvisa/cortical_surface/surface_tools/mesh_watershed.py", line 79, in watershed
idx=np.arange((vert.size)/3).reshape((vert.size)/3,1) # vertices index
TypeError: 'float' object cannot be interpreted as an integer
Exception ignored in: <function TemporaryDiskItem.del at 0x7f9f4558d900>
Traceback (most recent call last):
File "/casa/install/python/brainvisa/data/neuroDiskItems.py", line 2756, in del
File "/casa/install/python/soma/singleton.py", line 88, in new
TypeError: Application.singleton_init() missing 2 required positional arguments: 'name' and 'version'
Exception ignored in: <function TemporaryDirectory.del at 0x7f9f4558d750>
Traceback (most recent call last):
File "/casa/install/python/brainvisa/data/neuroDiskItems.py", line 2699, in del
TypeError: 'NoneType' object is not callable`

"I'm confused about which variable corresponds to the "NoneType" in the error messages, and what the 'float' object is. I'm using all default parameters, so I'm not sure if I've set some incorrect inputs?"

Really appreaciated for any help !

Thanks !

[denisri]

It seems that this code has not been properly ported and tested for python3. in the source file /casa/install/python/brainvisa/cortical_surface/surface_tools/mesh_watershed.py there are several occurrences of vertex.size/3 or (vertex.size)/3 which in python3 is a float result, and should be vertex.shape[0] instead.

[denisri]

I have pushed a fix in the sources but I don't know it it will be enough since I have not tested it and I have not run the process on my side.
The updated file can be found here:
https://brainvisa.info/download/updates/5.1.1/python/brainvisa/cortical_surface/surface_tools/mesh_watershed.py
To use it, you will have to perform a read/write install (I guess you are using a singularity/apptainer image of brainvisa):
run the bv command with no arguments from outside the container, it should open a GUI, where in the "Image" section you can perform a read/write install: it will copy all brainvisa files on the host filesystem, thus use about 2 GB of additional disk space. Then you can download the updated file above, and save/copy it at the same location in <brainvisa_install_dir>/install/ (so here in <brainvisa_install>/install/python/brainvisa/cortical_surface/surface_tools/).
But as I said, there might be other problems later...

[HusBunia]

Hi densiri:

Thanks for your help ! !

I also tried run the python scripts in brainvisa-4.6.1 with python2.7, it gaves me the same error (seems the code was built in a more old version ). I found the easiest way to fix the problem is add .astype(int) after variables should be looped as an integer, a litter similar with your modified scripts. I guess the sulcal basins extraction pipeline in 4.6.1 and 5.1.1 seems not very different, is it ?

after download files according to your instruction, I also seek a way to load brainvisa library in a python idel for convenient version error debug. If I want to use the scripts in 5.1.1, I believe your worried would be true... I used bv command to load a idel like pycharm outsied the container, but only the soma-base were found in loaded enviroment.

I greatly hope that a fixed version can be used in the near future ......

[denisri]

The sulcal basins extraction pipelines are not different between 4.6 and 5.1, you're right. There has been very little evolution in the toolboxes during the last years.
I'm a bit surprised the error was the same using python2.7, but anyway this code was kind of wrong, so it's better with the fix. Could you run it with the patched file (either mine or yours) ?
Using an IDE is possible, however there is the virtual container layer problem: the IDE itself runs outside of the container, but you need it to run code inside the container. Some IDEs can deal with this indirection, I know VSCode does it, I don't know for PyCharm (personally I do it the old way, using a source code editor which is not an IDE, and testing in an ipython shell, or using scripts, or a notebook, running inside the container). The problem is that code run from the IDE should not use the python command found in the host system path, but (at least) run bv python, or run an interactive environment inside the brainvisa container (bv).
Now if you are a developer and like to benefit from updates, you might consider installing a developer environment (using casa-dev containers and building from sources sync'd using git).
Last, for the brainvisa program (the axon project, actually), processes run from the GUI or via axon-runprocess, they need the axon environment loaded before the API can be used interactively. There are 2 ways of doing it;

• from the GUI, use the menu "File/Open shell": it will open an interactive ipython shell in a qtconsole widget
• from a regular shell (or ipython, or jupyter notebook): you need to run this code to initialize brainvisa/axon environment:

  from brainvisa.axon import processes
  processes.initializeProcesses()
  from brainvisa.processes import *
  

  then you can instantiate and run brainvisa processes. I don't know if it's what you were asking about...

[HusBunia]

In version 4.6.1, after adding the necessary .astype(int), the code runs successfully. After executing the watershed and area filtering with default parameters, the resulting single subject basin atlas looks like this:

I haven't run a complete watershed in Python 3 yet (as it's quite time-consuming..). It seems that the adaptive watershed algorithm could also provide me with the correct group brain atlas because it calls the same function just replace the vert_area with basin density map.

Thank you for your suggestion, I learned a lot. VSCode is more suitable for my current machine, at least for my current task.

Thanks for your help again !