mni2atlas

FSL Anatomical Labels for MNI Vector/ROI

FSL Anatomical Labels for MNI Vector/ROI. Mni2atlas takes an ROI or a vector of coordinates (both in the MNI space) and returns labels from different FSL atlases.

In VECTOR modality labels are returned in probability values (same results of FSL atlas tool).

In ROI modality the probability value reported for a label represents the frequency of that label in the roi for a given threshold of the FSL atlas probability map (0, 25 or 50; default = 25).

HOW TO USE
mni2atlas(VECTOR/ROI) the first input can be a MNI vector or an ROI in the MNI space. Depending on the input the script switches between two different work modalities. With no other input the script will seek labels among all available fsl atalses.

mni2atlas(VECTOR/ROI,ATLAS_SELECTOR) allows to choose among the following atlases:

Juelich Histological Atlas
Harvard-Oxford Cortical Structural Atlas
Harvard-Oxford Subcortical Structural Atlas
JHU ICBM-DTI-81 White Matter labels
JHU White Matter tractography Atlas
Oxford Thalamic Connectivity Atlas
Cerebellar Atlas in MNI152 after FLIRT
Cerebellar Atlas in MNI152 after FNIRT
MNI Structural Atlas

ATLAS_SELECTOR must be a row vector (i.e. [1,3,6]). Default value is [1:1:9]. You can also leave it as an empty vector (i.e. (VECTOR/ROI,[])).

[ATLAS]=MNI2ATLAS(VECTOR/ROI,...) the script returns the structure ATLAS whit the following fields: .name (of the atlas), .labels (a cell vector). No stdout will be print.

mni2atlas(VECTOR) prints on screen labels found for the MNI VECTOR position.

mni2atlas(ROI) prints on screen labels found for the input ROI. ROI can be a preloaded (with load_nii) volume or the path of a nifti volume.

ACKNOWLEDGEMENTS
This function uses some of the available FSL atlases