NITRC 1000 Functional Connectomes Project Forum: indi

Missing DWI JSON sidecar for ABIDE II BNI_1 dataset

Bahar Selimbeyoglu — Mon, 13 Jul 2026 13:22:31 GMT

<p class="PDq2pG_selectionAnchorContainer" data-start="118" data-end="124">Hello,</p>
<p data-start="126" data-end="214">I am working with the <strong data-start="148" data-end="166">ABIDE II BNI_1</strong> dataset and noticed that the DWI files include:</p>
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<pre class="cm-content q9tKkq_readonly m-0"><code>sub-30151_ses-1_run-1_dwi.nii.gz<br>
sub-30151_ses-1_run-1_dwi.bvec<br>
sub-30151_ses-1_run-1_dwi.bval</code></pre>
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<p data-start="324" data-end="346">but the corresponding:</p>
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<pre class="cm-content q9tKkq_readonly m-0"><code>dwi.json</code></pre>
is missing from the original dataset.</div>
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<p data-start="431" data-end="567">The DWI file contains 33 volumes, and the <code data-start="473" data-end="480">.bvec</code> and <code data-start="485" data-end="492">.bval</code> files also contain 33 entries, so they appear to be internally consistent.</p>
<p data-start="569" data-end="634">From the acquisition protocol, I found the following information:</p>
<p data-start="569" data-end="634"><em>Scanner: Philips Ingenia 3T Slice orientation: transverse Fold-over direction: AP Fat shift direction: P ... </em></p>
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<p class="PDq2pG_selectionAnchorContainer" data-start="902" data-end="1005">However, I am not sure how to convert the Philips protocol information into the correct BIDS value for:</p>
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<pre class="cm-content q9tKkq_readonly m-0"><code><span class="ͼz">"PhaseEncodingDirection"</span>: <span class="ͼz">"j"</span></code></pre>
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or: <br>
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<pre class="cm-content q9tKkq_readonly m-0"><code><span class="ͼz">"PhaseEncodingDirection"</span>: <span class="ͼz">"j-"</span></code></pre>
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<br>I also do not want to estimate fields such as <code data-start="1145" data-end="1163">TotalReadoutTime</code> or <code data-start="1167" data-end="1189">EffectiveEchoSpacing</code><br><strong>Could anyone from the ABIDE team, the BNI site, or anyone who has worked with this dataset share the original DWI JSON metadata or confirm the correct <code data-start="1364" data-end="1388">PhaseEncodingDirection</code> and other required DWI metadata?</strong><br>
<p data-start="1423" data-end="1457" data-is-last-node="" data-is-only-node="">Thank you very much for your help!</p>
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Missing DWI JSON sidecar for ABIDE II BNI_1 dataset

Bahar Selimbeyoglu — Mon, 13 Jul 2026 13:20:34 GMT

<p class="PDq2pG_selectionAnchorContainer" data-start="118" data-end="124">Hello,</p>
<p data-start="126" data-end="214">I am working with the <strong data-start="148" data-end="166">ABIDE II BNI_1</strong> dataset and noticed that the DWI files include:</p>
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<pre class="cm-content q9tKkq_readonly m-0"><code>sub-30151_ses-1_run-1_dwi.nii.gz
sub-30151_ses-1_run-1_dwi.bvec
sub-30151_ses-1_run-1_dwi.bval</code></pre>
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<p data-start="324" data-end="346">but the corresponding:</p>
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<pre class="cm-content q9tKkq_readonly m-0"><code>dwi.json</code></pre>
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<p data-start="392" data-end="429">is missing from the original dataset.</p>
<p data-start="431" data-end="567">The DWI file contains 33 volumes, and the <code data-start="473" data-end="480">.bvec</code> and <code data-start="485" data-end="492">.bval</code> files also contain 33 entries, so they appear to be internally consistent.</p>
<p data-start="569" data-end="634">From the acquisition protocol, I found the following information:</p>
<p data-start="569" data-end="634"><em>Scanner: Philips Ingenia 3T Slice orientation: transverse Fold-over direction: AP Fat shift direction: P ... </em></p>
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<div class="pointer-events-none absolute end-1.5 top-1 z-2 md:end-2 md:top-1">
<p class="PDq2pG_selectionAnchorContainer" data-start="902" data-end="1005">However, I am not sure how to convert the Philips protocol information into the correct BIDS value for:</p>
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<pre class="cm-content q9tKkq_readonly m-0"><code><span class="ͼz">"PhaseEncodingDirection"</span>: <span class="ͼz">"j"</span></code></pre>
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<p data-start="1050" data-end="1053">or: </p>
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<pre class="cm-content q9tKkq_readonly m-0"><code><span class="ͼz">"PhaseEncodingDirection"</span>: <span class="ͼz">"j-"</span></code></pre>
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<p data-start="1099" data-end="1211">I also do not want to estimate fields such as <code data-start="1145" data-end="1163">TotalReadoutTime</code> or <code data-start="1167" data-end="1189">EffectiveEchoSpacing</code></p>
<p data-start="1213" data-end="1421"><strong>Could anyone from the ABIDE team, the BNI site, or anyone who has worked with this dataset share the original DWI JSON metadata or confirm the correct <code data-start="1364" data-end="1388">PhaseEncodingDirection</code> and other required DWI metadata?</strong></p>
<p data-start="1423" data-end="1457" data-is-last-node="" data-is-only-node="">Thank you very much for your help!Scanner: Philips Ingenia 3T</p>
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RE: Problems with downloading the indi data

Dev Bansal — Mon, 08 Jun 2026 16:48:48 GMT

<p>Hi,<br>      I faced problems of downloading the data set <a href="http://fcon_1000.projects.nitrc.org/indi/retro/cobre.html" target="_blank" rel="noopener">http://fcon_1000.projects.nitrc.org/indi/retro/cobre.html</a> . It returns the message "This tool/resource's administrator will have to grant you permission to view this page.". I have registered as a nitrc user, and also send the indi access request, and i have got the reply . Can anyone tell me what happen, how can i fix it? thks.</p>

ABIDE Composite Phenotypic File - Won't Download

Morgan O'Donnell — Wed, 04 Feb 2026 18:08:03 GMT

<p>Hi everyone! I can't seem to get the ABIDE I Composite Phenotypic File to download. Does anyone know why or where I can get this information? </p>
<p>Currently, it will open a new window on my browser then close. Nothing downloads. </p>

RE: NEURO-BUREAU: ADHD-200 Processed Data Release

Zheng Zhao — Sun, 04 Jan 2026 11:35:59 GMT

<p class="isSelectedEnd">Dear </p>
<p class="isSelectedEnd">I hope this message finds you well. I am currently conducting a research project focused on ADHD, and I would like to kindly request access to the preprocessed ADHD-200 dataset.</p>
<p class="isSelectedEnd">Specifically, I am interested in obtaining the preprocessed resting-state fMRI ROI time series data based on the AAL atlas. These ROI-level time series would be highly valuable for the methodological components of my study, particularly for functional connectivity analysis and graph-theoretical modeling.</p>
<p class="isSelectedEnd">I would be grateful if you could let me know whether these AAL-based fMRI time series are available, and if so, whether there are any requirements, forms, or data usage agreements that need to be completed in order to obtain access.</p>
<p class="isSelectedEnd">Thank you very much for your time and consideration. I look forward to your response.</p>
<p>Kind regards,<br>Zhao Zheng</p>
<p>zhaozheng0226@126.com</p>

RE: NEURO-BUREAU: ADHD-200 Processed Data Release

Alireza Abyar — Wed, 03 Dec 2025 8:40:45 GMT

<p class="MsoNormal"><strong><span style="font-size: 10.5pt; line-height: 115%; font-family: ";">Dear <br><br></span></strong></p>
<p class="MsoNormal"><strong><span style="font-size: 10.5pt; line-height: 115%; font-family: ";">Hello</span></strong></p>
<p class="MsoNormal"><strong><span style="font-size: 10.5pt; line-height: 115%; font-family: ";">I hope you are doing well.i am currently conducting a research project on ADHD and wpuld like to kindley request access to the preprocessed ADHD-200 dataset .if available these data would significantly support the methodological steps in my study ,particulary in fnctional  connectivity and graph  -theoretical analysis .please let me know if there are any requirements or forums I need to complete for obtaining access.</span></strong></p>
<p class="MsoNormal"><strong><span style="font-size: 10.5pt; line-height: 115%; font-family: ";"> thank you for your time and assistance.</span></strong></p>
<p class="MsoNormal"><strong><span style="font-size: 10.5pt; line-height: 115%; font-family: ";">best regards</span></strong></p>
<p class="MsoNormal"><strong><span style="font-size: 10.5pt; line-height: 115%; font-family: ";">Alireza Abyar</span></strong></p>
<p class="MsoNormal"> </p>

RE: Follow-up on COBRE Data Access Request Submitted on October 19, 2025

FCP/INDI Admin — Fri, 07 Nov 2025 18:25:26 GMT

<p>Hi, have you requested access to both:</p>
<ul>
<li>https://www.nitrc.org/project/request.php?group_id=296</li>
<li>https://www.nitrc.org/project/request.php?group_id=404</li>
</ul>
<p> </p>
<p><em>Originally posted by Lintang Linggarjati:</em></p>
<blockquote>
<p> Dear Moderator,</p>
<p> </p>
<p>I am writing to follow up on the data access request I submitted on October 19, 2025, regarding the COBRE dataset (<a href="https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html">https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html</a>). This dataset is very important as I intend to use it for my undergraduate thesis research. I have not yet received a response and would like to confirm whether my request has been received.</p>
<p>Here are the steps I took to request access to the COBRE dataset:</p>
<p>1. I created a NITRC account using my institutional email address (<a href="mailto:lintang.linggarjati-2022@fst.unair.ac.id">lintang.linggarjati-2022@fst.unair.ac.id</a>).</p>
<p>2. I accessed the COBRE project page on NITRC (<a href="https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html">https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html</a>).</p>
<p>3. I clicked the “Here” button as per the “NITRC Download Instructions” (Figure 1) and filled out the data use agreement form, stating that the dataset would be used for my undergraduate thesis research.</p>
<p>4. After submission, I received a confirmation message (Figure 2). I clicked the link that redirected me back to the NITRC website, and a message appeared in a yellow box (Figure 3).</p>
<p> </p>
<p>Does the text in the yellow box indicate that my request is still in process and pending? However, a week has passed, and I have not received any further updates since then.</p>
<p>Please let me know if there are any additional steps I need to take from my side to process this request or if I should contact the FCON_1000/INDI group directly.</p>
<p>I hope you can reply quickly because this is very important to me and there is a deadline. I would greatly appreciate it if you could provide an update on the status of my request at your earliest convenience.</p>
<p>Thank you for your help.</p>
<p> </p>
<p>Best regards,</p>
<p>Lintang Linggarjati</p>
<p>Faculty of Science and Technology</p>
<p>Airlangga University</p>
<p>Indonesia</p>
</blockquote>
<p> </p>

Follow-up on COBRE Data Access Request Submitted on October 19, 2025

Lintang Linggarjati — Thu, 30 Oct 2025 7:37:50 GMT

<p> Dear Moderator,</p>
<p> </p>
<p>I am writing to follow up on the data access request I submitted on October 19, 2025, regarding the COBRE dataset (<a href="https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html">https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html</a>). This dataset is very important as I intend to use it for my undergraduate thesis research. I have not yet received a response and would like to confirm whether my request has been received.</p>
<p>Here are the steps I took to request access to the COBRE dataset:</p>
<p>1. I created a NITRC account using my institutional email address (<a href="mailto:lintang.linggarjati-2022@fst.unair.ac.id">lintang.linggarjati-2022@fst.unair.ac.id</a>).</p>
<p>2. I accessed the COBRE project page on NITRC (<a href="https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html">https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html</a>).</p>
<p>3. I clicked the “Here” button as per the “NITRC Download Instructions” (Figure 1) and filled out the data use agreement form, stating that the dataset would be used for my undergraduate thesis research.</p>
<p>4. After submission, I received a confirmation message (Figure 2). I clicked the link that redirected me back to the NITRC website, and a message appeared in a yellow box (Figure 3).</p>
<p> </p>
<p>Does the text in the yellow box indicate that my request is still in process and pending? However, a week has passed, and I have not received any further updates since then.</p>
<p>Please let me know if there are any additional steps I need to take from my side to process this request or if I should contact the FCON_1000/INDI group directly.</p>
<p>I hope you can reply quickly because this is very important to me and there is a deadline. I would greatly appreciate it if you could provide an update on the status of my request at your earliest convenience.</p>
<p>Thank you for your help.</p>
<p> </p>
<p>Best regards,</p>
<p>Lintang Linggarjati</p>
<p>Faculty of Science and Technology</p>
<p>Airlangga University</p>
<p>Indonesia</p>

Pre-processed data ABIDE II

marjan safari — Thu, 09 Oct 2025 3:27:07 GMT

Where can I download the pre-processed data ABIDE II ?

RE: rs-fMRI analysis for ABIDE data miss slice acquirement time

olfa Adouni — Mon, 29 Sep 2025 18:23:10 GMT

<p><em>Originally posted by Lin Lin :</em></p>
<blockquote>
<p>Dear all, </p>
<p>When I attempted to preprocess rs-fMRI  from the ABIDE dataset, I found that the islice acquirement time were missing from both the scanning procdedures and the parameters information file. Additionaly, The raw data is not in BIDS format, which is required by the most preprocess pipeline such as C-PAC.</p>
<p>As a results, the slice timeing correction step cannot be performed, which may significantly affect the accuracy of  time-series anaylsis. If anyone has located the slice acquirement times elsewhere or has suggestions on how to proceed, I would greatly appreciate your guidance. </p>
<p>Sincerely, </p>
<p>Lin</p>
</blockquote>
<p> </p>