Hippocampus field in ADNIMERGE file

[guise...@gmail.com]

Hi all,

I was trying to obtain the ADNI2 subjects' hippocampus volume from the ADNIMERGE file but I would like to know in which file was the original data before the merge.

It is said that it is "UCSF Hippocampus" but in the file "UCSFNTVOL.csv" there are not RID from subjects that started in ADNI2 and these have data in the field "Hippocampus" in ADNIMERGE.

Thank you in advance,

Güise.

[Danielle J Harvey]

The UCSF Hippocampal data would be from the FreeSurfer file – I’m guessing that ADNIMERGE uses cross-sectional FreeSurfer, so you’ll find the original data in the cross-sectional FreeSurfer file for ADNIGO/2…

 

The UCSFSNTVOL file only contains data from ADNI-1 and due to the time-intensiveness of that process, it was stopped part way through ADNI-1 and FreeSurfer was used instead…

 

Danielle

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[guise...@gmail.com]

First of all, thank you for your quickly response.

I'm seeing the data of the Cross-Sectional FreeSurfer (5.1) file (UCSFFSX51_11_02_15_V2.csv) but I don't see a field called "Hippocampus" as in ADNIMERGE. 

I've observed that there are some fields called "Hippocampal Subfields Volume of..." but, for example, in the subject with RID 4005 only the field ST131HS which is the "Hippocampal Subfields Volume of LeftCA1" according to the table dictionary has a bigger value (both are measured in mm3) than the field "Hippocampus" that is in ADNIMERGE, which should be the whole volume.

It seems weird.

[Naomi Saito]

Hi Güise,

You can find "adnimerger.r" in R folder in "Merged ADNI 1/GO/2 Packages for R" (ADNIMERGE_0.0.1.tar.gz), and this code tells us how ADNIMERGE data is created. 

In line 343: ucsfvol$Hippocampus <- (ucsfvol$ST29SV + ucsfvol$ST88SV)

From checking UCSFFSX51_DICT,

ST29SV: Subcortical Volume (aseg.stats) of LeftHippocampus

ST88SV: Subcortical Volume (aseg.stats) of RightHippocampus

Also, I understand that ADNIMERGE uses newest data, and "UCSFFSX51_08_01_16.csv" is the newest version of UCSFFSX51. 

Naomi

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From: adni...@googlegroups.com <adni...@googlegroups.com> on behalf of guise...@gmail.com <guise...@gmail.com>
Sent: Friday, June 16, 2017 4:01 AM

To: Alzheimer's Disease Neuroimaging Initiative (ADNI) Data

Subject: Re: [adni-data] Hippocampus field in ADNIMERGE file

 

[guise...@gmail.com]

Hi Naomi,

Thank you for the answer, I will check the R folder next time!

[Leonie]

Hello,

also using these data (ucsfvol$Hippocampus <- (ucsfvol$ST29SV + ucsfvol$ST88SV)),
I was wondering if you have any recommendations with regard to dichotomizing the hippocampal volumes in normal vs atrophic.
In the literature I find cut-off values for LEAP hippocampal volumes (<5·389 cm3, Vos et al., 2015), but not for these Freesurfer data.
In addition, what scaling variable should be used to adjust for ICV? Should these values even be adjusted at all?

Thank you in advance!

Best, Leonie

Op vrijdag 16 juni 2017 17:37:30 UTC+2 schreef guise...@gmail.com: