quqixun / brainprep

Preprocessing pipeline on Brain MR Images through FSL and ANTs, including registration, skull-stripping, bias field correction, enhancement and segmentation.

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brainprep's Issues

N4BiasFieldCorrection issues

I encountered the following problem when running bias_correction.py
OSError: No command "N4BiasFieldCorrection" found on host ubuntu. Please check that the corresponding package is installed.

But I have successfully installed ANTs, and when I try to run which antsRegistration* in the terminal, it returns the Ant installation directory /opt/ANTs/bin//antsRegistration

So how to solve the problem? Looking forward to your reply，thx!

scripts shouldn't have code that will run if imported

In general scripts shouldn't run functions when imported, which is what would happen with the scripts located in src/.

To only run code when being called as a script (and not from the import function) use:

if __name__ == '__main__':
    # run functions here

This will prevent code being run if the user wishes to import the functions defined within the modules.

hi

hi there are some code cant use

scns are in one file

GM,WM, and CSF all three are in one file. can you please tell how you separate all three and save in separate Dicom or nifti files

No command "N4BiasFieldCorrection" found on host kim-X10DAi. Please check that the corresponding package is installed.

Thanks for your work，but an error occurred when I run bias_correction

No command "N4BiasFieldCorrection" found on host kim-X10DAi. Please check that the corresponding package is installed.

Can't Find the dataset used

I registered on the site you gave for the dataset but I can't find your dataset inside the website. Can you give any further indications, please?

Qustions about application in general brain preprocessing

Hi, I want to apply the pipeline to process nomral mri with 1 nii file for each subject. But I currently has no access to test dataset used in the profile, I am not clear about the reorganize and registration part, wether they work the same or just to skip the steps. A little bit explaination about relationship between NC1/2 and AD1/2 can help a lot, like whether they are from the same subject at diffrent stage and whether they are different modalities. Thanks!