Missing FreeSurfer brainmask images

[Batuhan Karaman]

Hello everyone,

I am trying to collect the FreeSurfer brainmask images of all the subjects who have their MRI volumetric information in adnimerge.csv. As far as I get, these images have the description "FreeSurfer Cross-Sectional Processing brainmask", in the image collections. I can find the images that have 1.5-Tesla strength. However, I cannot find the 3-Tesla scans and the images which have missingness in the field strength column in adnimerge.csv. I was wondering how I can obtain those images? Thank you for the support!

Best regards,

Batuhan 

[Naomi Saito]

Hi Batuhan,

I understand that ADNIMERGE uses MRI volumetric information from UCSF FreeSurfer data. 

1.5T from UCSFFSX_mm_dd_yy.csv

3.T from UCSFFSX51_mm_dd_yy.csv (for ADNI1, 2, GO), and UCSFFSX6_mm_dd_yy.csv (for ADNi3). 

These files are under the MR Image Analysis section. 

Naomi

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From: adni...@googlegroups.com <adni...@googlegroups.com> on behalf of Batuhan Karaman <kb...@cornell.edu>
Sent: Thursday, October 20, 2022 11:47 AM
To: Alzheimer's Disease Neuroimaging Initiative (ADNI) Data <adni...@googlegroups.com>
Subject: [adni-data] Missing FreeSurfer brainmask images

 

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[Batuhan Karaman]

Hey Naomi,

Thanks for the clarification. However, I'm actually trying to find the post-processed (skull-stripped and intensity normalized) brainmask images, i.e., not the volume/surface area information extracted from those images by segmentation.

Batuhan

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[Danielle J Harvey]

Hi Batuhan,

 

It doesn’t look like these FreeSurfer masks were uploaded after ADNI-1.

 

Danielle

To view this discussion on the web visit https://groups.google.com/d/msgid/adni-data/CAEspXmeZ3t5EmvTOhsHWQo7CZsP%2BUP5Vcio3RQ8YrgkA4H283Q%40mail.gmail.com.

[Batuhan Karaman]

Hello Dr. Harvey,

Thank you so much for the clarification. I did not realize that. Do you know if there is a way for me to get the images from later ADNI phases? I thought I could contact the UCSF cohort to see if they store the images in their own servers.

Best regards,

Batuhan

[Danielle J Harvey]

Hi Batuhan,

 

You can certainly email the UCSF lab to find out – you can find the contact information in the methods document for their FreeSurfer summaries that have been posted on the Study Data page.

To view this discussion on the web visit https://groups.google.com/d/msgid/adni-data/013ebaae-bab6-4a29-9110-569e4777b25dn%40googlegroups.com.

[Batuhan Karaman]

Yes, I know that document. Thank you so much for your help!

Batuhan