NITRC NITRC Community Forum: open-discussion

OASIS3 - individual scan acquisition year and country

Daniel Franco — Thu, 09 Jul 2026 13:21:00 GMT

Hi all,
Is there a way to obtain the acquisition year for each scan (or at least the year of baseline per subject, so that I can derive a year of image acquisition)? Similarly, is country of residence available? I'm assuming all participants reside within the United States.
I'm currently needing this data to assign contextual features in my analysis.
Thanks in advance, Daniel

spmT on 3d render visibility

Arshad Zaman — Mon, 06 Jul 2026 17:09:50 GMT

Hi, 
Does anyone know if it is possible to improve spm activations to better be  visible on the 3d render view? while in A+C+S activations apprear fine, on the render brain image the surface activations are bearly visible. I know one can play around with the depth/Azimuth functions for repective cross sections, however those are only really useul if you can also see the surface activations clearly too. is there anyway to bring the sruface activations actually onto the sruface of the 3d rendered brain? I have played around with options, darkest, brightest, etc but no joy. I have seen a few online tutorials, however there too the surface activations are not clearly visible at all.
Any suggesitons will be much appreciated.
Bw,
Arshad

Subject: Fully HIPAA compliant Deployment for OASIS-3 Longitudinal Data Mapping

MohammedYusuf Modan — Mon, 06 Jul 2026 17:09:50 GMT

<div class="paragraph normal ng-star-inserted" data-start-index="702">Hi Saif,</div>
<div class="paragraph normal ng-star-inserted" data-start-index="708">We have the exact technical infrastructure required to instantly accelerate your OASIS-3 neuroimaging research and ADRC Clinical Data workflows.</div>
<div class="paragraph normal ng-star-inserted" data-start-index="852">To ensure your study can efficiently map subject IDs and calculate "days-from-entry" alignments to the corresponding MRI/PET sessions, we can deploy a dedicated, locked-down research "Spoke" tailored specifically for your team.</div>
<div class="paragraph normal ng-star-inserted" data-start-index="1079">Our Research Setup Engine will bypass the burden of building a local data environment so you can focus entirely on selecting the clinical assessments closest to each imaging session. Your deployment will include:</div>
<ul class="ng-star-inserted">
<li class="paragraph list-item normal ng-star-inserted" data-start-index="1291">Secure Python FastAPI Backend: A dedicated, containerized environment to safely and rapidly execute your longitudinal data parsing and mapping scripts.</li>
<li class="paragraph list-item normal ng-star-inserted" data-start-index="1442">The BigQuery "Evidence Lake": A highly secure, centralized data storage pool designed for sub-second data retrieval and structuring complex, multi-year datasets.</li>
<li class="paragraph list-item normal ng-star-inserted" data-start-index="1603">Zero-Trust Processing & Ephemeral Memory: Our architecture ensures that data processing sessions are instantly wiped from local memory once your data is securely routed to the Evidence Lake, maintaining absolute data privacy.</li>
</ul>
<div class="paragraph normal ng-star-inserted" data-start-index="1828">Additionally, should your neuroimaging research ever scale into active clinical application, please note that this same infrastructure natively supports our advanced AI clinical documentation and autonomous compliance monitoring modules, which can be activated on demand.</div>
<div class="paragraph normal ng-star-inserted" data-start-index="2099">Let us know if you would like us to provision this secure environment for your study, and we can immediately initiate the setup.</div>
<div class="paragraph normal ng-star-inserted" data-start-index="2099"> </div>
<div class="paragraph normal ng-star-inserted" data-start-index="2099">Best,</div>
<div class="paragraph normal ng-star-inserted" data-start-index="2099">— Manager, Quantum Security Syndicate-m Ascent Enterprise, LLC Secure Posture Portal: www.quantumaudit.health Direct Support: support@quantumaudit.health</div>

Clinical Toolbox for SPM - Troubleshooting

Kilian Frohlich — Thu, 02 Jul 2026 13:18:53 GMT

Dear Community,
I have been using the clinical toolbox for years. Now, it produced following error the first time:
clinical_mrnormseg ERROR: Dimension mismatch 
 
Anyone familiar with this? 
 
Yours!

RE: Question about clinical labels in OASIS-3

saif_khan — Mon, 29 Jun 2026 15:20:01 GMT

I will download the ADRC Clinical Data spreadsheet and use the subject ID together with the days-from-entry information to match the clinical assessments to the corresponding MRI/PET sessions. Since OASIS-3 is longitudinal, I will select the clinical assessment closest to each imaging session when assigning labels.
Thank you also for pointing me to the Imaging Data Dictionary and the ADRC Clinical Data documentation. This information is very useful for my study.

RE: Question about clinical labels in OASIS-3

wissal ghachem — Mon, 29 Jun 2026 13:57:03 GMT

Hi,
the cognitive/diagnostic status isn't produced by a command-line script — it lives in the clinical data tables you download from the OASIS-3 data browser as spreadsheets (CSV). The download scripts only fetch the imaging/FreeSurfer/PUP files; they don't generate labels.
There are two places to look, both in the ADRC Clinical Data table:
<ol class="[li_&]:mb-0 [li_&]:mt-1 [li_&]:gap-1 [&:not(:last-child)_ul]:pb-1 [&:not(:last-child)_ol]:pb-1 list-decimal flex flex-col gap-1 pl-8 mb-3">
<li class="font-claude-response-body whitespace-normal break-words pl-2">CDR (Clinical Dementia Rating) global score — the quickest "normal vs. impaired" flag:
<ul class="[li_&]:mb-0 [li_&]:mt-1 [li_&]:gap-1 [&:not(:last-child)_ul]:pb-1 [&:not(:last-child)_ol]:pb-1 list-disc flex flex-col gap-1 pl-8 mb-3">
<li class="font-claude-response-body whitespace-normal break-words pl-2">CDR = 0 → cognitively normal</li>
<li class="font-claude-response-body whitespace-normal break-words pl-2">CDR = 0.5 → very mild impairment (commonly treated as MCI / at-risk)</li>
<li class="font-claude-response-body whitespace-normal break-words pl-2">CDR ≥ 1 → dementia (1 mild, 2 moderate, 3 severe)</li>
</ul>
</li>
<li class="font-claude-response-body whitespace-normal break-words pl-2">dx1–dx5 (coded clinician diagnosis) — more specific than CDR because it gives the etiology. <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">dx1</code> is the primary diagnosis, with values like "Cognitively normal", "AD dementia", "vascular dementia", plus contributing factors (mood disorder, vitamin deficiency, etc.). So "at risk of AD" specifically means a CDR > 0 with <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">dx1</code> pointing toward AD dementia / uncertain dementia, rather than just any impairment.</li>
</ol>
How to get it:
<ol class="[li_&]:mb-0 [li_&]:mt-1 [li_&]:gap-1 [&:not(:last-child)_ul]:pb-1 [&:not(:last-child)_ol]:pb-1 list-decimal flex flex-col gap-1 pl-8 mb-3">
<li class="font-claude-response-body whitespace-normal break-words pl-2">Open the OASIS-3 project in the data browser (central.xnat.org).</li>
<li class="font-claude-response-body whitespace-normal break-words pl-2">Load the Subjects and ADRC Clinical Data tables.</li>
<li class="font-claude-response-body whitespace-normal break-words pl-2">Export as a Spreadsheet (CSV). You'll get columns like <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">cdr</code>, <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">dx1</code>–<code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">dx5</code>, <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">mmse</code>, <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">ageAtEntry</code>, plus a session label.</li>
</ol>
One important detail: OASIS-3 is longitudinal, so each clinical row is tagged with the subject ID + "days from entry" (the <code class="bg-text-200/5 border border-0.5 border-border-300 text-danger-000 whitespace-pre-wrap rounded-[0.4rem] px-1 py-px text-[0.9rem]">dXXXX</code> suffix), and a subject's status can change over time. To label a given scan, match by subject ID and pick the clinical assessment closest in days-from-entry to that MR/PET session.
All of this is documented in the OASIS-3 Imaging Data Dictionary (the "ADRC Clinical Data / dx1–dx5" and CDR sections) on oasis-brains.org.
Hope this helps.

Question about clinical labels in OASIS-3

bash — Mon, 29 Jun 2026 12:53:17 GMT

How can I identify whether each subject is cognitively normal or at risk of Alzheimer's disease? Is this information available through a command-line script, or in a separate file?

OASIS-3 ASL Acquisition Parameters (Bolus Duration, TI1/TI2, Labeling Duration) Missing – Where Can I Find Them?

Kardelen Aktas — Mon, 08 Jun 2026 16:49:43 GMT

Hello everyone,
I am working with the OASIS-3 dataset and would like to process the ASL images quantitatively. However, I could not find several important acquisition parameters in the available metadata, including:
Bolus duration (labeling duration)
TI1 and TI2 (or equivalent inversion times / post-labeling delays)
Labeling scheme details (PASL, pCASL, etc.)
Other ASL sequence parameters required for CBF quantification
I checked the dataset documentation and image metadata available to me, but these parameters do not appear to be included.
Has anyone identified where these ASL acquisition parameters can be obtained? Are they available in the original DICOM headers, a separate documentation file, or through direct contact with the OASIS-3 team?
Any guidance would be greatly appreciated.
Thank you!

OASIS-3 resting-state fMRI/BOLD preprocessing pipeline

Yunier Prieur Coloma — Tue, 05 May 2026 18:09:15 GMT

Dear Community,
I downloaded the raw resting-state fMRI/BOLD data from OASIS-3 and would like to obtain clean ROI-level time series for FC and sliding-window dFC/FCD analyses.
My main focus is not fMRI preprocessing itself, but I need a reliable and reasonably user-friendly workflow for this purpose. I am considering fMRIPrep,SPM12,CONN, or similar tools, but I am not sure which one is most appropriate for OASIS-3.
Also, are preprocessed resting-state fMRI/BOLD data or ROI-level time series already available for OASIS-3?
Best regards,
Yunier

RE: Unable to access OASIS-3 data even though I've been granted access

oasisadmin — Fri, 10 Apr 2026 15:32:41 GMT

Originally posted by Kexin Gao:
<blockquote>
I was granted access to OASIS-3 on NITRC as a User on August 13, 2024. However, I am currently unable to access the Image Repository, which appears as “protected data.”
</blockquote>
Dear OASIS User,
We hope this message finds you well. In support of recent directives by the National Institutes of Health (NIH), OASIS Project Managers updates focused on protecting data provided by NIH Controlled-Access Data Repositories (CADRs), including OASIS-3 and OASIS-4. 
In response to the NIH directive, OASIS project managers are currently removing individuals from countries of concern from these projects. NIH is prohibiting access to and ending any remaining ongoing projects involving NIH CADRs and associated data for researchers and institutions located in certain countries. These countries of concern include China (including Hong Kong and Macau), Russia, Iran, North Korea, Cuba, and Venezuela, consistent with Executive Order 14117 and 28 CFR Part 202 “Preventing Access to U.S. Sensitive Personal Data and Government-Related Data by Countries of Concern or Covered Persons.”  
Regrettably, we must inform you that your access to the OASIS-3 and OASIS-4 projects has been revoked. This action is necessary to comply with the updated security regulations and ensure the integrity of the data provided by NIH CADRs.
For more details regarding these changes, please refer to the Guide Notice NOT-OD-25-083. Should you have any questions or require further clarification, you are encouraged to reach out to the NIH support team at <a href="mailto:gds@mail.nih.gov">gds@mail.nih.gov</a>.
We apologize for any inconvenience this may cause and appreciate your understanding and cooperation in adhering to these necessary security measures.