2024_Ruthe_SND/input

Inputs

• C57BL6_mouse folder: The corresponding atlas folder from DSI Studio. This folder can also be found in the root directory where DSI Studio is installed.
• C57BL6_mouse_iso.nii.gz: This is the iso NIFTI file created by loading the fib file from the C57BL6_mouse folder and saving the iso part of it as a NIFTI file. This file is equivalent to the C57BL6_mouse.ISO.nii.gz file in the C57BL6_mouse folder, which has a higher resolution. However, since the masks were drawn using the C57BL6_mouse.fib.gz file, this was saved separately.
• NP_template_sc0.nii.gz: This is our in-house MRI template, also known as MTPL. Reference link to the paper: Frontiers in Neuroinformatics, and the GitHub repository: Aswendt-Lab/AIDAmri - SND_Mask_trafu branch.
• ABtemplate_website.nii.gz: This was downloaded to be able to overlay it with viral tracing data and compare it with the masks drawn.
• 12_wks_coronal_100141780_100um_projection_density.nrrd: Containes viral tracing projection data. (fits on ABtemplate_website).