NITRC WFU_PickAtlas Forum: help

RE: Error using spm_slice_vol (line 32) spm_slice_vol.c not compiled - see Makefile

Rainer Boegle — Wed, 14 Jan 2026 7:48:15 GMT

<p>Does anyone have the source files such that we could just compile these ourselves?</p>
<p>Best wishes,</p>
<p>Rainer</p>

RE: Problem with WFU PickAtlas Results Viewer

Yoshikazu Nakano — Mon, 17 Nov 2025 6:03:57 GMT

<p data-start="102" data-end="130">Hi huilee92 and scchester,</p>
<p data-start="137" data-end="245">I just encountered exactly the same error with WFU_PickAtlas “Results Viewer” under SPM12 + MATLAB R2024a:</p>
<div class="contain-inline-size rounded-2xl relative bg-token-sidebar-surface-primary">
<div class="sticky top-9">
<div class="absolute end-0 bottom-0 flex h-9 items-center pe-2">
<div class="bg-token-bg-elevated-secondary text-token-text-secondary flex items-center gap-4 rounded-sm px-2 font-sans text-xs"> </div>
</div>
</div>
<div class="overflow-y-auto p-4" dir="ltr"><code class="whitespace-pre! language-text">Using SPM8_lite, adding (spm_lite) to path.
Warning: Name is nonexistent or not a directory: …/spm_lite
…
ERROR │ wfu_results_defaults │ Line 0052: Array dimensions must agree.
</code></div>
</div>
<p data-start="469" data-end="580">From extensive debugging I found the cause: in <strong data-start="516" data-end="544"><code data-start="518" data-end="542">wfu_results_defaults.m</code></strong>, around line 46-53 the code does:</p>
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<div class="sticky top-9">
<div class="absolute end-0 bottom-0 flex h-9 items-center pe-2">
<div class="bg-token-bg-elevated-secondary text-token-text-secondary flex items-center gap-4 rounded-sm px-2 font-sans text-xs"> </div>
</div>
</div>
<div class="overflow-y-auto p-4" dir="ltr"><code class="whitespace-pre! language-matlab">hind = <span class="hljs-built_in">find</span>(h >= <span class="hljs-number">0</span>);
vind = <span class="hljs-built_in">find</span>(v >= <span class="hljs-number">0</span>);
screenIndex = <span class="hljs-built_in">min</span>(<span class="hljs-built_in">find</span>(hind == vind));
</code></div>
</div>
<p data-start="690" data-end="861">In MATLAB R2024a (and in some multi-monitor setups) the vectors <code data-start="754" data-end="760">hind</code> and <code data-start="765" data-end="771">vind</code> may differ in length, so <code data-start="797" data-end="809">hind==vind</code> leads to the “Array dimensions must agree” error.</p>
<p data-start="868" data-end="917"><strong data-start="868" data-end="875">Fix</strong>: replace that block with something like</p>
<div class="contain-inline-size rounded-2xl relative bg-token-sidebar-surface-primary">
<div class="sticky top-9">
<div class="absolute end-0 bottom-0 flex h-9 items-center pe-2">
<div class="bg-token-bg-elevated-secondary text-token-text-secondary flex items-center gap-4 rounded-sm px-2 font-sans text-xs"> </div>
</div>
</div>
<div class="overflow-y-auto p-4" dir="ltr"><code class="whitespace-pre! language-matlab">idx = <span class="hljs-built_in">intersect</span>(hind, vind);
<span class="hljs-keyword">if</span> <span class="hljs-built_in">isempty</span>(idx)
screenIndex = <span class="hljs-number">1</span>;
<span class="hljs-keyword">else</span>
screenIndex = idx(<span class="hljs-number">1</span>);
<span class="hljs-keyword">end</span>
</code></div>
</div>
<p data-start="1053" data-end="1155">After applying this patch and restarting MATLAB, the Results Viewer now works correctly in my setup.</p>
<p data-start="1162" data-end="1301">If you like, I can share the full patched <code data-start="1204" data-end="1228">wfu_results_defaults.m</code> and my version details (MATLAB R2024a, SPM12 r7771, PickAtlas 3.0.5b).</p>
<p data-start="1162" data-end="1301">Note: If you're searching for <code data-start="1387" data-end="1411">wfu_results_defaults.m</code>: it's located in <code data-start="1429" data-end="1455">.../wfu_results/private/</code> — being under a <code data-start="1472" data-end="1482">private/</code> folder, it won't show up using <code data-start="1514" data-end="1521">which</code> or <code data-start="1525" data-end="1531">edit</code> unless called from the parent function.</p>
<p data-start="1308" data-end="1365"> </p>
<p data-start="1308" data-end="1365">Hope this helps you too!</p>
<p data-start="1308" data-end="1365">Best wishes,</p>
<p data-start="1308" data-end="1365">Yoshikazu Nakano</p>

RE: Error using spm_slice_vol (line 32) spm_slice_vol.c not compiled - see Makefile

learningfmri — Tue, 26 Aug 2025 19:20:21 GMT

<p>Hi! Also having this issue and using SPM 25 on a Mac. Has there been any resolution for it? Thanks!</p>

RE: Error using spm_slice_vol (line 32) spm_slice_vol.c not compiled - see Makefile

Mehran Zare-Bidoky — Sat, 19 Jul 2025 14:24:42 GMT

<p><em>Originally posted by Stephanie Anakwe:</em></p>
<blockquote>
<p>Having this error message come up when I try to open an atlas. I am using a Mac</p>
</blockquote>
<p>Same here. Are you using WFU PickAtlas with SPM12 or SPM25? I suspect the issue is that WFU PickAtlas hasn’t been updated for SPM25 yet.</p>

WFU_Pickatlas in SPM25 is not working

Mehran Zare-Bidoky — Sat, 19 Jul 2025 14:22:40 GMT

<p>Hi,<br><br>It seems WFU_Pickatlas is not updated for SPM25 yet. I also changed my SPM version to 12, but it still doesn't work. My MATLAB version is r2024a.<br><br>Is the problem from my side?</p>

Error using spm_slice_vol (line 32) spm_slice_vol.c not compiled - see Makefile

Stephanie Anakwe — Tue, 24 Jun 2025 16:17:31 GMT

<p>Having this error message come up when I try to open an atlas. I am using a Mac</p>

RE: Problem saving masks

Joyce Oerlemans — Wed, 21 Aug 2024 11:55:02 GMT

Brodmann area 12 not visible

Rasha Alharthi — Sat, 03 Aug 2024 9:10:26 GMT

<p>I am encountering an issue with the WFU-PickAtlas tool while attempting to use it for ROI-to-ROI analysis in the CONN Toolbox. Specifically, when selecting Brodmann area 12 from the available regions of interest (ROIs), it does not appear in the display region. All other Brodmann areas are visible and display correctly.</p>
<p><strong>Additional Question:</strong> Regarding the use of the dilate tool in PickAtlas, is it appropriate to use this tool? If so, how should it be applied, and what impact might it have on my results in CONN Toolbox? Could using the dilate tool negatively affect the accuracy or validity of my analysis?</p>
<p>As a beginner in this field, I would greatly appreciate any guidance or recommendations on how to resolve this issue.</p>
<p>Thank you, Rasha</p>

Table Generation Statistics Meaning

cmvomo — Fri, 10 May 2024 0:37:41 GMT

<p>Hi,</p>
<p> </p>
<p>I'm using WFU to get average SUV in the putamen  (using smoothed 18FDG PET files as input).</p>
<p> </p>
<p>To do so, I select the region (HUMAN ATLAS->brodmann areas+ -> I chose putamen both side), and use generate table to get the average SUV in that region for each participant. </p>
<p>Everything works fine but I was wondering whether the value in the average column of the tbl file corresponds to the actual mean SUV ?</p>
<p> </p>
<p>Thank's in advance</p>

RE: Problem saving masks

lidizpe — Thu, 25 Apr 2024 13:44:15 GMT

<p>Hi!!</p>
<p>Did you ever get the answer? I'm having the same problem when trying to dilate my mask.</p>
<p> </p>
<p>Thanks,</p>
<p>Lidia</p>