NailMonkey

Generate mask of an individual macaque monkey through NIMH D99 Atlas Note that the template inside D99 is as same as the Saleem & Logotheis atlas book: A Combined MRI and Histology Atlas of the Rhesus Monkey

Installation

• install FSL
• install nipype (might be not necessary in the future)
• Atlas (D99 is already embedded in the program)

Example

The example file is taken from PRIME-MRM dataset Newcastle_prime-mrm/0000001/session_1/anat_1/.

The DICOM images should be transformed into nii file first. If you are using Ubuntu, you can use dcm2nii to do the job. 3DSlicer can also finish the job.

sudo apt install dcm2nii

run.py file gives an example code to run a dataset contained in ./data_example/anta.nii

OFC 13b (306) and LIPv (329) are shown here.

Several files are generated:

• rec_anta.nii.gz orientation rectified nii file in rectified space
• bet_anta.nii.gz brain extracted nii file in original space
• betrec_anta.nii.gz brain extracted orientation rectified nii file in rectified space
• tpl_bet_rec_anta.nii.gz brain extracted orientation rectified nii file in D99 template space
• mask_306_13b_rec_anat.nii.gz mask of the OFC 13b area in rectified space
• mask_329_LIPv_rec_anat.nii.gz mask of the OFC 13b area in rectified space
• mask_306_13b_anat.nii.gz mask of the OFC 13b area in original space
• mask_329_LIPv_anat.nii.gz mask of the OFC 13b area in original space
• tpl_betrec_anat.mat the transformation matrix from the rectified space to template space
• tpl_betrec_anat_inv.mat the transformation matrix from the template space to rectified space
• tpl_betrec_bet_anat.mat the transformation matrix from the rectified space to original space
• tpl_EBZ_rec_anat.txt ear bar zero (EBZ) in rectificed original space defined in D99 template
• tpl_EBZ_anat.txt ear bar zero (EBZ) in original space defined in D99 template
• merged_mask_rec_anat.nii.gz merged mask in rectified space
• merged_mask_anat.nii.gz merged mask in original space

Figures

• LIPv
• OFC 13b

Atlas

You can use other atlas but it means you need to deeply modify the program. Atlas_generation.ipynb is used to generate files in D99_mask.

Current Issues

• The auto orientation detection is not correct for now, you need try different orientations using dims option in ProcessNiiFile function.
• Only tested in macOS Monterey 12.5/13.2.1 with zsh