help > Measurement of entire volume brain and Roi
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Mar 11, 2020  03:03 PM | Luca Cuffaro - University of East London, NeuroRehabiliation Unit
Measurement of entire volume brain and Roi

I am working retrospectively on MRI of stroke patients - project of neurorehabilitation. These images are from clinical admission/discharge of these patients, so I don't have nice series (e.g. just the axial and the sagittal are T1 and none MP-RAGE) to merge all plans and perform an efficient normalization/segmentation. I have mapped the lesion and created VOIs using just the optimal axial one I have for all of them.

1. How can I calculate the entire volume of brain using Mricron? (I cannot use MRIcroGL because I had a old graphics card in this pc)
2. Following: draw->descriptive of VOIs in Mricron, are the results shown already calculated in cc, don't they?

Thanks for every reply!
May 22, 2020  06:05 PM | Chris Rorden
RE: Measurement of entire volume brain and Roi
1. I would use a tool like SPM's segmentation to segment the brain from the other tissue, and segment different tissue types in the brain. This will generate probability maps for each voxel for 0..1 (0%..100%) for gray matter, white matter and CSF. The sum for each volume will reveal the volume of each tissue type. This is better than a binary classification of each voxel as it solves the partial volume problem (e.g. voxels that are partly gray and partly white matter).

2. For a drawing in MRIcron, choose Draw/Descriptive to see the volume of your region. For example

Center of mass XYZ 106.00x126.00x106.00
VOI nvox(cc)=min/mean/max=SD: 33401 33.40 =25.0000 96.8260 120.0000 = 23.1273
suggests your drawing submsumes 33401 voxels or 33.4 cubic centimeters