- This topic has 1 reply, 2 voices, and was last updated 5 years, 9 months ago by sychoi.
June 14, 2017 at 8:53 am #743mvtr76Participant
Hi! Thanks a lot to provide this sensational software!!
Please, I have some doubts and i really would apreciate some help!
I did the Surface/Volume Registration of the file 2523412.nii.gz, part of the Beijing Enhanced dataset.
1) What label or data should i use to get the volumetry of the Brain?
2) When I compute the volumes ( “ROI Details” tab of the “Mask Tool”) of the 2523412.hemi.labell.ni.gz i have these results:
1 cerebrospinal fluid 584,2226 (cc)
2 grey matter 580,657 (cc)
3 white matter 89,7777 (cc)
4 grey matter/CSF 96,2268 (cc)
5 grey matter/white matter 54,7521 (cc)
6 csf/other 50,2301 (cc)
Using this same file 2523412.nii.gz in other software online (volBrain) i get different results:
White Matter (WM) 516.02 (34.88%)
Grey Matter (GM) 798.20 (53.95%)
Cerebro Spinal Fluid (CSF) 165.34 (11.18%)
Brain (WM + GM) 1314.23 (88.82%)
Intracranial Cavity (IC) 1479.57 (100.00%)
I would like to use the BrainSuite also to get a kind of Volumetry Report , what should i do?
How should i report the grey matter of the brain, if there are “grey matter 580,657 (cc)”, “grey matter/CSF 96,2268 (cc)” and “grey matter/white matter 54,7521 (cc)”?
Thanks a lot!!
June 19, 2017 at 6:46 pm #745sychoiParticipant
The hemi.label file is an intermediate file that we use to roughly identify regions of the brain. If you load the hemi.label.nii.gz file in brainsuite, you will see that it labels the right and left brainstem, cerebrum, and a general subcortical area.
You can take a look at your tissue classification results by opening the pvc.label.nii.gz or pvc.frac.nii.gz
Here’s a video where I explain the brainsuite outputs: http://brainsuite.org/video-tutorials/checking-outputs/
In order to get calculations of GM/WM/CSF and total volume, run your subject through SVReg which can be run on the GUI or command line. (instructions found here: http://brainsuite.org/processing/svreg/)
it will output a roi.stats.txt file which outputs volume measurements which you can open in excel. the 1st line will give you total CSF volume, 2nd: GM Vol and 3rd WM Vol.
It will also list regional measurements and you can find the description of the ROI IDs by opening the brainsuite_labeldescription.xml
It looks like for this subject I get
BrainSuite uses partial volume tissue classification which considers that some voxels are composed of mixed tissue and assigns it that way. So a single voxel can be calculated as 40% GM and 60% WM which is why you get voxels labeled as GM/WM or GM/CSF. This can give you more accurate measurements.
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