Hi,


I am using the IBSR V2.0 Dataset for my experiments. I am unable to find the individual segmentation code for each tissue i.e. gray matter, white matter and CSF. Kindly help me in this regard. Where actually it is defined.

for example: for image volume contained in IBSR_01_ANALYZE.tgz which file contains the segmentation code from which I can compute the segmentation metrices.


Thanks and Regards,
Sayan

Hi Sayan,

Perhaps you downloaded "IBSR_V2.0 skull-stripped NIfTI" where the README.txt file does not describe everything.  Please look at the README.txt file in "IBSR_V2.0".

Andy.

Hi Andy,


            I have downloaded the "IBSR_V2.0" and downloaded the README.txt as well. I case of IBSR_01_ANALYZE.tgz, it contains "images" and "segmentation" folders. In "segmentation" two files are there namely, "IBSR_01_segTRI_ana" and "IBSR_01_seg_ana". which file contains the actual ground truth. If I am not wrong, in the README.txt the ground truth contains RGB values and also no truth value for GM. Please help me to find the ground truth values as I am unable to understand the same. It will be great for me. Lastly, what about the file "IBSR_01parc_ANALYZE.tgz".


Thanks..

Sayan

Originally posted by Sayan Kahali:

Hello,

The README.txt file does give RGB, but that is not the important part.  The first number in the list, the "Fill_Value", gives the integer that you will find in the IBSR_01_seg_ana.img file.  This number indicates which neuroanatomical region is present for each voxel in the 3D image volume file (*.img).  For example, when a voxel has a value of 3, that means there is "Left-Cerebral-Cortex" at that location.

The RGB values are provided so that a color lookup table can be created.  This will allow IBSR segmentations to be displayed in the colors used by Freesurfer.

If you are looking for gray matter (GM), cerebral cortex is gray matter, but so is the caudate, and other regions.  Some regions are a mixture of gray and white matter.  The files called, e.g. "IBSR_01_segTRI_ana.img" show the brain segmented into background = 0, CSF=1, gray matter = 2, and white matter = 3.  The README.txt file gives the mapping of which segmented regions map to GM, WM, and CSF.

The file "IBSR_01parc_ANALYZE.tgz" is the parcellation of cerebral cortex into regions based on gyral and sulcal landmarks.  There you can find specific cortical regions like "FP" which is the frontal pole.  The abbreviations follow Freesurfer (see https://academic.oup.com/cercor/article/14/1/11/433466).

Note that the IBSR parcellations were created manually by outlining regions slice-by-slice in the 3D volume using software called "cardviews."  These are not Freesurfer parcellations which are created automatically based on surfaces.

Andy.
Originally posted by dalvinder kaur: