Dataset features description

[vfdev-5]

Hi,
I was just wondering whether somewhere there is a more detailed and structured description of data features? For example, what is participants_site ?
Thanks

[alrzmshy]

I second that. Domain knowledge would be very helpful for this challenge as there are people that are not familiar with the description of features.

[glemaitre]

Participants site are the hospital where the acquisition have been done.

[glemaitre]

@alirezamosh check also the website. If you have more questions we can discuss in more details.

[vfdev-5]

@glemaitre concerning "anatomy" features this site has been already sited in one of the issues. Maybe it would good to include it as a reference for those who is not famiiliar with the domain.

[glemaitre]

I see.

@GaelVaroquaux Do you think that it should be added in a sort of introduction in the notebook or shall we have a wiki or an aside page info for those features. I am scared to clutter the notebook by adding up information.

[vfdev-5]

I am scared to clutter the notebook by adding up information.

This information can be stored in a additional file, for example

[glemaitre]

This information can be stored in a additional file, for example

Yep I had in mind the following suggestion:

• an additional file.
• an additional webpage on the main site.
• on the wiki page of the repository.

[vfdev-5]

Another question for brain anatomy specialists, according to wiki it seems there are 4 ventricles:

• lateral ventricles right and left (one for each hemisphere)
• third ventricle
• fourth ventricle

However in the data we have also anatomy_5th-Ventricle column with data like:

EDIT: seems FreeSurfer speaks about the 5th ventrice too :

BrainSegNotVent - same as BrainSeg without ventricles (lateral, inferior lateral, 3rd, 4th, 5th), CSF, and choroid plexus.

[glemaitre]

@vfdev-5 You are right. The extraction was done with FreeSurfer so you will find information there regarding the anatomy.

[glemaitre]

@vfdev-5 you can let this issue opened. This is actually useful and this is not a duplicate.

[akatav]

I am wondering what the following anatomical features mean (are they thickness or area or volume measures ?)

• anatomy_Left-Lateral-Ventricle
• anatomy_Left-Inf-Lat-Vent
• anatomy_Left-Cerebellum-White-Matter
• anatomy_Left-Cerebellum-Cortex
• anatomy_Left-Thalamus-Proper
• anatomy_Left-Caudate
• anatomy_Left-Putamen
• anatomy_Left-Pallidum
• anatomy_3rd-Ventricle
• anatomy_4th-Ventricle
• anatomy_Brain-Stem
• anatomy_Left-Hippocampus
• anatomy_Left-Amygdala
• anatomy_CSF
• anatomy_Left-Lateral-Ventricle
• anatomy_Left-Inf-Lat-Vent
• anatomy_Left-Cerebellum-White-Matter
• anatomy_Left-Cerebellum-Cortex
• anatomy_Left-Thalamus-Proper
• anatomy_Left-Caudate
• anatomy_Left-Putamen
• anatomy_Left-Pallidum
• anatomy_3rd-Ventricle
• anatomy_4th-Ventricle
• anatomy_Brain-Stem
• anatomy_Left-Hippocampus
• anatomy_Left-Amygdala
• anatomy_CSF
• anatomy_Left-VentralDC
• anatomy_Left-vessel
• anatomy_Left-choroid-plexus
• anatomy_Right-Lateral-Ventricle
• anatomy_Right-Inf-Lat-Vent
• anatomy_Right-Cerebellum-White-Matter
• anatomy_Right-Cerebellum-Cortex
• anatomy_Right-Thalamus-Proper
• anatomy_Right-Caudate
• anatomy_Right-Putamen
• anatomy_Right-Pallidum
• anatomy_Right-Hippocampus
• anatomy_Right-Amygdala
• anatomy_Right-VentralDC
• anatomy_Right-vessel
• anatomy_Right-choroid-plexus
• anatomy_5th-Ventricle
• anatomy_WM-hypointensities
• anatomy_Left-WM-hypointensities
• anatomy_Right-WM-hypointensities
• anatomy_non-WM-hypointensities
• anatomy_Left-non-WM-hypointensities
• anatomy_Right-non-WM-hypointensities
• anatomy_Optic-Chiasm
• anatomy_CC_Posterior
• anatomy_CC_Mid_Posterior
• anatomy_CC_Central
• anatomy_CC_Mid_Anterior
• anatomy_CC_Anterior

[vfdev-5]

For more info on fsMRI, connectivity I found the article "Learning and comparing functional connectomes across subjects" and "Nilearn docs" somehow helpful.

HTH

[romainVala]

@suprsankr
those measures are volume because they are not in the cortex (only cortical area are defined between 2 surface which allow the quantification of mean thickness and area)

[akatav]

@romainVala thank you! i did not quite understand the second part of the answer. The above measures are also volume measures (such as anatomy_Optic-Chiasm..) except that they are not part of the cortex. So these regions cannot conveniently be measured for a thickness and area measure.
However for a non brain scientist, it suffices to know that the above measures are just volume measures. correct ? :)

[romainVala]

yes