Some Mindboggle-101 dataset v3 labels.DKT31.manual+aseg.MNI152.nii.gz files contain labels 1000, 2000, 1001, 2001, 1032, 2032, 1033, and 2033

[br-cpvc]

Dear Mindboggle project maintainers.

I am currently trying to use the Mindboggle-101 dataset v3 'labels.DKT31.manual+aseg.MNI152.nii.gz' volume label files from https://osf.io/9ahyp/ as the basis for a multi-atlas segmentation.

During this work I have discovered that some of the Mindboggle-101 'labels.DKT31.manual+aseg.MNI152.nii.gz' files contain labels that I belive should not be included, as described in https://mindboggle.readthedocs.io/en/latest/labels.html as:

Four labels have been removed from the 35 cortical labels (“ctx-“) of the Desikan-Killiany (DK) protocol (see footnote #1): bankstss (1001, 2001), corpus callosum (1004, 2004), frontal pole (1032, 2032), and temporal pole (1033, 2033).

The following files contain the listed labels which properbly should not be included:

Extra-18_volumes/HLN-12-2: 1033 2033
Extra-18_volumes/HLN-12-3: 2032
Extra-18_volumes/HLN-12-5: 2032
Extra-18_volumes/HLN-12-8: 2033
Extra-18_volumes/HLN-12-9: 2032
Extra-18_volumes/HLN-12-12: 1032
MMRR-21_volumes/MMRR-21-1: 1032 1033
MMRR-21_volumes/MMRR-21-6: 1001
MMRR-21_volumes/MMRR-21-9: 2032
MMRR-21_volumes/MMRR-21-10: 2001
MMRR-21_volumes/MMRR-21-17: 2032
MMRR-21_volumes/MMRR-21-19: 1033
MMRR-21_volumes/MMRR-21-20: 2033
NKI-RS-22_volumes/NKI-RS-22-10: 1033
NKI-RS-22_volumes/NKI-RS-22-12: 1033 2033
NKI-RS-22_volumes/NKI-RS-22-13: 1033
NKI-RS-22_volumes/NKI-RS-22-18: 2033
NKI-RS-22_volumes/NKI-RS-22-22: 1033
NKI-RS-22_volumes/NKI-RS-22-9: 2033
OASIS-TRT-20_volumes/OASIS-TRT-20-2: 1033
OASIS-TRT-20_volumes/OASIS-TRT-20-3: 2033
OASIS-TRT-20_volumes/OASIS-TRT-20-4: 1033
OASIS-TRT-20_volumes/OASIS-TRT-20-6: 2033
OASIS-TRT-20_volumes/OASIS-TRT-20-10: 1032
OASIS-TRT-20_volumes/OASIS-TRT-20-12: 2032 2033
OASIS-TRT-20_volumes/OASIS-TRT-20-14: 2033
OASIS-TRT-20_volumes/OASIS-TRT-20-16: 1001
OASIS-TRT-20_volumes/OASIS-TRT-20-20: 2032

I am not sure if these labels being present in the 'labels.DKT31.manual+aseg.MNI152.nii.gz' output files is a problem in only for the Mindboggle-101 data project or if it is actually a bug in the Mindboggle segmentation code. This is my primary reason for posting the problem here.

I would also like to report these findings to the Mindboggle-101 data project but I cannot seem to find were such infomation should be posted. The page https://mindboggle.info/data.html# link to where the code for this project is hosted, but non of the sites seem to have a active community page or link. Do anyone know where the right place to report this to the Mindboggle-101 data project is?

As I am a programmer and do not have much clinical expertise, manually make non trivial corrections to these regions is out of the scope for me, but I can read in the article: https://www.frontiersin.org/articles/10.3389/fnins.2012.00171/full that the labels: bankstss (1001, 2001), corpus callosum (1004, 2004), frontal pole (1032, 2032), and temporal pole (1033, 2033) should be redistributed into other labels:

Banks of superior temporal sulcus [removed]
The area in the banks of the superior temporal sulcus in the DK protocol has been redistributed to the superior and middle temporal gyri.

Frontal pole [removed]
The area included in the DK frontal pole region has been redistributed to the superior frontal and orbitofrontal gyri.

Temporal pole [removed]
The area included in the DK temporal pole has been redistributed to the superior, middle, and inferior temporal gyrus regions.

Additionally, I also found that all of the 'labels.DKT31.manual+aseg.MNI152.nii.gz' label files contain the labels 1000 and 2000. These two labels are not described in the list https://mindboggle.readthedocs.io/en/latest/labels.html which makes me belive that they should not be present in the output. Would it be correct to remove these by setting them to 0, or should 1000, and 2000 also be redistributed into other labels?

[amygutierrez]

Hello,
Thank you for bringing this to our attention! I will be looking over this issue and will get back with any feedback.

[br-cpvc]

Are there any news regarding the problems that I have described above? Have I reported this the correct way/place or should it be reported elsewhere/to someone else?