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ALXXLARG / FCT

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Remove usage of nii_tools #1

Closed lawlessrd closed 2 years ago

lawlessrd commented 2 years ago

The niitools package used in this pipeline are outdated and often result in errors and incorrect data. Please remove all uses of niitools functions (load_nii, load_untoch_nii, save_untoch_nii), and replace them with either the built in matlab functions (niftiread, niftiwrite) or the appropriate spm functions (spm_vol, spm_reslice). If you need a reference for how some of these functions are used, please see the finalized SCZ_WM main function here: https://github.com/lawlessrd/SCZ-WM-pipeline/blob/main/matlab/src/scz_main.m. Additionally, here is a link to a repo of the SPM functions which may be of use to you (though you won't have to add these to the repo, they should already be in the SPM12 package, this is just a helpful reference/example).

Let me know if you have any questions.

lawlessrd commented 2 years ago

Forgot to include the SPM link: https://github.com/VUIIS/spm_readwrite_nii

ALXXLARG commented 2 years ago

OK. I will do that. Thanks!

lawlessrd commented 2 years ago

No problem. If you need any help with removing these functions or github in general feel free to reach out.

ALXXLARG commented 2 years ago

OK!

ALXXLARG commented 2 years ago

Hello,

I think I have removed all uses of niitool functions. I am wondering if you could have a look. Please let me know if there are any more issues.

Thank you very much for your help!