Missing reslice_template file in the repository

[braahkrayem]

Hello,

I was exploring the Toolkit_for_MIRA_LAB_Striatal_Segmentation repository and noticed that the reslice_template file in the StriatalSegmentation folder appears to contain only zero values, which isn't useful for my purpose. I am looking for a valid reslice_template that can be used for reslicing MRI data as intended.

Could you please upload a proper reslice_template file or provide guidance on where I can find a working version of this file? If this is available in another part of the repository or in a different repository, a link would be much appreciated.

Thank you in advance for your help!

[jocwilliams]

Hello, thank you for your interest in this segmentation pipeline.

It is intentional that that reslice_template.nii contains all zero data values, as it is not required for reslicing. Reslicing only requires the image geometry, which is intact in that file. You can see how it works on line 99 of main_CNNStriatalSegmentation and line 260 of the function getReslicedCNN_image in the same .m file. The purpose of this reslice is to ensure that the image being provided to the pipeline matches the data on which the CNN was trained.

For reslicing your imaging data, you should use any image that is in the space and resolution that you want. For example, if you have preprocessed resting-state fMRI data you would like to reslice to, you can choose any resting-state run from the preprocessed dataset. My main suggestion is to try and make sure you are reslicing to the data you are using it with. This pipeline uses SPM, so you can see how we do it from the aforementioned functiongetReslicedCNN_image function, but other software can reslice as well.

Best,
John