help > Segmentation Results in IBSR Data
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Jun 24, 2019  04:06 PM | Merve Tan
Segmentation Results in IBSR Data
Dear NITRC users,

I am using a pipeline to measure the volumes of cortex GM, WM, ventricular CSF and extra-ventricular (sulcal) CSF. To do so, I do segmentation on T1W brain MRI. I would like to use the ground truth data to evaluate the accuracy of this pipeline.

What I need is not a comparison to other software (e.g. Freesurfer), but instead to check if the pipeline provides accurate and consistent volumetric calculations of these structures. Therefore, I need volumetric results of the ground truth data for each of these structures.

I downloaded the IBSR 2.0 skull-stripped NIFTI, IBSR_V2.0, 20 Normals. When I open these files, I can see the segmentations very well (as attached). However, I cannot find a file that directly gives the volumetric results as cm^3 or number of voxels corresponding to each segmented structure. (e.g. Left ventricle --- cm^3, R WM --- cm^3).

I read the README file and saw that UnZip may cause an artifact. But, I am using "the Unarchiver" for Mac and "7Zip" for Windows. Also, the otl file is empty.


Is there a file that gives the direct volumetric results of these segmented structures? Thank you.


Best,
Merve
Jun 25, 2019  08:06 AM | Andrew Worth
RE: Segmentation Results in IBSR Data
Hello Merve,

Sorry, there is no such file that provides the volumes.  As you probably know, the way to do it is to count the voxels for each tissue and multiply by the voxel volume for that scan.

Andy.
Jul 6, 2019  04:07 PM | Merve Tan
RE: Segmentation Results in IBSR Data
Originally posted by Andrew Worth:
Hello Merve,

Sorry, there is no such file that provides the volumes.  As you probably know, the way to do it is to count the voxels for each tissue and multiply by the voxel volume for that scan.

Andy.


Hello Andrew,

Thank you very much for your response. I keep that in mind. Sorry about my late response.


Best regards,
Merve