Understanding the standardized MRI data sets

[Anja Zgodic]

Good evening everyone, 

I apologize in advance for this question, it is probably naive but I do not come from the brain imaging area of study, rather from biostatistics. My question is simple, I would like to understand whether the standardized MRI datasets are ready to use as is? Or whether I need to apply additional processing to them. Here is the link to the standardized MRI dataset explanation: https://adni.loni.usc.edu/methods/mri-tool/mri-analysis/#mri-data-set-container 

Thank you so much for your insight, 

Anja

[Naomi Saito]

Hi Anja,

I understand that standardized MRI datasets will tell you which RID have complete sets in ADNI1 or which image files to use (i.e. imageID seriesID)

For example, if you use the file "ADNI_Complete1YearVisitList####.csv)  file, it will tell you which subjects (RID) are 1-year completers (screen, month6 and month12 scans). 

It does not include actual MRI results.  When I want to use MRI volumetric data, I use UCSF FreeSurfer data (UCSFFSX for 1.5T, UCSFFSX51 for 3T ADNI1GO2, UCSFFSX6 for ADNI3). 

ADNIMERGE file also includes MRI volumetric values from FreeSurfer data. 

Naomi

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From: adni...@googlegroups.com <adni...@googlegroups.com> on behalf of Anja Zgodic <anja_...@alumni.brown.edu>
Sent: Monday, May 1, 2023 4:34 PM
To: Alzheimer's Disease Neuroimaging Initiative (ADNI) Data <adni...@googlegroups.com>
Subject: [adni-data] Understanding the standardized MRI data sets

 

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[Danielle J Harvey]

Thanks Naomi!

 

Anja,

 

Also, if you plan to work with the images themselves, using the predefined collections, rather than the list of RIDs/VISCODES that Naomi describes to identify the numeric summaries derived from those images (say from FreeSurfer), you will need to decide if you want to do any more preprocessing. The images have already undergone motion correction, etc. by the MRI core. It has been a while since those collections were put together, but if I remember correctly, there are some instances in which more than 1 scan is included in the collection for the same RID/VISCODE. You can refer to the publication that describes these collections (PMCID: PMC3891834) for more information.

 

Danielle

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[Anja Zgodic]

Thank you very much Naomi and Danielle, your help is much appreciated! 

Anja

[Anja Zgodic]

I am following up with a question on the standardized MRI datasets. I was able to download the standardized images from the ADNI1:Complete 1Yr 1.5T collection. I notice that depending on the processing/"description", e.g. "MPR-R; ; N3; Scaled", "MPR-R; GradWarp; B1 Correction; N3; Scaled", "MPR-R; GradWarp; N3; Scaled" etc, the images have (similar but) different dimensions. I was wondering if there was a way to reconcile images from different processing or if I am misunderstanding and I should only be using a specific processing/"description".

To be clear, the "description" is a column that I see in the table of the ADNI1:Complete 1Yr 1.5T collection where we select the files we want to download. Feel free to ask clarifying questions if something does not make sense.

Thank you very much for your help,
Anja