vanandrew/brainextractor

A re-implementation of FSL's Brain Extraction Tool in Python

brainextractor's Issues

Python stops unexpectedly

$ brainextractor pp01_mp2rage_whole_brain_t1_std_defaced.nii.gz 1.nii.gz
Initializing...
Parameters: bt=0.500000, d1=20.000000, d2=10.000000, rmin=3.330000, rmax=10.000000
tmin: 0.000000, t2: 0.000000, t: 312.700000, t98: 3127.000000, tmax: 3999.000000
Center-of-Mass: [115.63921706 142.84159284 172.89465062]
Head Radius: 161.157240
Median within Head Radius: 1692.000000
Initializing surface...
Brain extractor initialization complete!
Running surface deformation...
Segmentation fault: 11

process finished with exit code -1073741819 (0xc0000005)

When I run BrainExtractor， sometimes the process stops suddenly with this：

process finished with exit code -1073741819 (0xc0000005)

How can I fix it？ And what caused it？

Thanks！

ValueError: could not broadcast input array from shape (185,219,150) into shape (185,219,0)

Hello, thanks for your good repository.

When i adjust the threshold lower than 0.5 (ex: 0.2, 0.3), it's not work.
For the same image, threshold =0.5 is work.

Need help on using Longitudinal MRI image as input

Hi,

I am working on skull-stripping for brain scan. I have cross-sectional and longitudinal MRI brain scans data. When I use cross-sectional data, the brainextractor shows good result. However, the brainextractor shows bad in longitudinal data.

When I start the brainextractor for longitudinal data, it shows UserWarning: The voxels in this image are non-isotropic! Brain extraction settings may not be valid!. So I view the pixdim in header, I get [-1. 1. 1. 2. 6.002 0. 0. 0. ].

What should I do for the python code when using brainextractor?

Thanks!

Array is too big error

Hello, thank you for a nice implementation. I found some bug/limitation on it.
With some images I am getting error.

[FD]   warnings.warn(
[FD] Traceback (most recent call last):
[FD]   File "/mnt/c/Users/h492884/PycharmProjects/slicer_MER/slicer_plugin/model/Resources/py/bet.py", line 13, in <module>
[FD]     bet.run()
[FD]   File "/home/user/slic_build/python-install/lib/python3.9/site-packages/brainextractor/main.py", line 287, in run
[FD]     self.step_of_deformation(
[FD] ValueError: array is too big; `arr.size * arr.dtype.itemsize` is larger than the maximum possible size.

Problem with running your code

Please explain why this error is coming and how to fix it. I am using Google Collab and after installing the brainextractor and cloning your github this error comes

:bug: Surface initialization fails on non-isotropic voxels

I am getting the following error while running the example, what is the reason?

Is it implemented by functions such as BET2? And I see the following functions in FSL.