NITRC NITRC Community Forum: open-discussion

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

<p class="isSelectedEnd">Hello everyone,</p>
<p class="isSelectedEnd">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:</p>
<p class="isSelectedEnd">Bolus duration (labeling duration)</p>
<p class="isSelectedEnd">TI1 and TI2 (or equivalent inversion times / post-labeling delays)</p>
<p class="isSelectedEnd">Labeling scheme details (PASL, pCASL, etc.)</p>
<p class="isSelectedEnd">Other ASL sequence parameters required for CBF quantification</p>
<p class="isSelectedEnd">I checked the dataset documentation and image metadata available to me, but these parameters do not appear to be included.</p>
<p class="isSelectedEnd">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?</p>
<p class="isSelectedEnd">Any guidance would be greatly appreciated.</p>
<p>Thank you!</p>

OASIS-3 resting-state fMRI/BOLD preprocessing pipeline

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

<p class="isSelectedEnd">Dear Community,</p>
<p class="isSelectedEnd">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.</p>
<p class="isSelectedEnd">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.</p>
<p class="isSelectedEnd">Also, are preprocessed resting-state fMRI/BOLD data or ROI-level time series already available for OASIS-3?</p>
<p>Best regards,</p>
<p>Yunier</p>

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

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

<p><em>Originally posted by Kexin Gao:</em></p>
<blockquote>
<p>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.”</p>
</blockquote>
<p class="MsoNormal" style="background: #F4F4F5;"><span style="font-family: '__Inter_Fallback_d65c78',serif; color: #334155;">Dear OASIS User,</span></p>
<p class="MsoNormal" style="background: #F4F4F5;"><span style="font-family: '__Inter_Fallback_d65c78',serif; color: #334155;">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),<u> including OASIS-3 and OASIS-4</u>. </span></p>
<p class="MsoNormal" style="background: #F4F4F5;"><span style="font-family: '__Inter_Fallback_d65c78',serif; color: #334155;">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. <strong>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.”  </strong></span></p>
<p class="MsoNormal" style="background: #F4F4F5;"><span style="font-family: '__Inter_Fallback_d65c78',serif; color: #334155;">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.</span></p>
<p class="MsoNormal" style="background: #F4F4F5;"><span style="font-family: '__Inter_Fallback_d65c78',serif; color: #334155;">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>.</span></p>
<p class="MsoNormal" style="background: #F4F4F5;"><span style="font-family: '__Inter_Fallback_d65c78',serif; color: #334155;">We apologize for any inconvenience this may cause and appreciate your understanding and cooperation in adhering to these necessary security measures.  </span></p>

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

Kexin Gao — Fri, 10 Apr 2026 15:03:03 GMT

<p>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.”</p>

RE: Connectivity question

Patrick Bedard — Fri, 13 Mar 2026 16:05:26 GMT

<p>ok thanks , </p>
<p>I was afraid this would be the case!!</p>
<p>I did chopped the timeseries ans selected specific blocks (frames); but now I have less timepoints and the data is not continuous anymore, so it's harder to do causality analysis, say like Granger or some other time-varying FC</p>

RE: Connectivity question

Rodolphe Nenert — Fri, 13 Mar 2026 15:49:37 GMT

<p>Different numbers of timepoints can matter because the connectivity estimates from longer series are usually more stable. I would not fix that by upsampling. A better approach is to compute connectivity from matched portions of the task across all subjects (for example the same blocks or the first common segment), convert correlations to Fisher z, and then compare groups at the second level. You can include the number of usable frames as a covariate only as a secondary sensitivity analysis, but not as the main solution if scan length is essentially confounded with group.</p>

RE: Connectivity question

Patrick Bedard — Fri, 13 Mar 2026 2:58:42 GMT

<p>Anna, </p>
<p>Thanks for responding!</p>
<p>I don't want to split the timeseries, I want to use all the timepoints (volumes) available. <br>But, this creates the issue of having many more timepoints for a group vs the other and so the correlations will be calculated with different number of timepoints.  </p>
<p>Just to be sure I'm cler, the correlation between ROI for the controls would be based on 480 timepoints while the correlation for the patients would be based on 240 timepoints. Then I'd compare between groups those correlations.</p>
<p>Is this a problem that these correlations are based on different timeseries length?</p>
<p>best</p>
<p>patrick</p>

RE: Connectivity question

Anna Farmer — Wed, 11 Mar 2026 16:42:56 GMT

<p>Patrick, </p>
<p>I mainly work with resting state fMRI, but I have a suggestion for addressing your issue. You can always use fslsplit to split out the time series into individual volumes and then use fslmerge to merge the volumes you want back into one file for analysis. You could script this so it manually removes the extra volumes from the end of the time series in your patients. </p>
<p>Hope this helps, </p>
<p>Anna </p>

Connectivity question

Patrick Bedard — Tue, 10 Mar 2026 18:48:35 GMT

<div>Hello expert,</div>
<div> </div>
<div>I have a question about fMRI connectivity analysis.</div>
<div>I’m trying to see if connectivity differs between groups of patient and controls, in a set of ROI.</div>
<div> </div>
<div>Say I'd use correlation </div>
<div> </div>
<div>My issue is that the fMRI timeseries are much longer for the control than patients, about 2 times longer, so more timepoints (~480 vs ~250); it's a feature of the task they were doing, the patients got fatigued much earlier. So, the correlation for the controls would be computed with more timepoints than the correlation of the patients.</div>
<div> </div>
<div>-1-</div>
<div>So, my question is since the number of timepoints differ substantially between the groups, is this a problem for group analysis? I would compare the correlation between groups with a t-test for example.</div>
<div> </div>
<div>-2-</div>
<div>If this an issue, is there a way out? Maybe up-sampling the patient time series or some other methods?</div>
<div> </div>
<div> </div>
<div>thansk a lot</div>
<div>patrick</div>
<div> </div>
<div> </div>

Loading AnalyzIR data into SPM

Henry Brice — Wed, 26 Nov 2025 20:57:42 GMT

<p>I want to use the gPPI module in SPM in order to run a task-based functional connectivity analysis om fNIRS data.</p>
<p>I have used the AnalyzIR (Huppert) toolbox to process the data, so I have the motion-corrected HbO and HbR timeseries arranged in ROI space, but I can't work out how to output that preprocessed data in a format that I can read into SPM, or any in-depth explanation of the data structure that the gPPI package wants to read in.</p>
<p>I'd be very grateful for any tips or tricks to get this to work.</p>
<p>Henry</p>