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Hello</div>
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My name is Adrianna Giuffre - I am a PhD candidate at the University of Calgary. </div>
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I am using SimNIBS for a current modelling project. </div>
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I am having the problems running new head models.</div>
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1) I am having troubles running the head models for any of my participants - I keep getting an error message saying : (screen shot attached)</div>
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<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures">Traceback (most recent call last):</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures"><span class="Apple-converted-space">
</span>File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in <module></span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures"><span class="Apple-converted-space">
</span>main()</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures"><span class="Apple-converted-space">
</span>File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures"><span class="Apple-converted-space">
</span>headmodel(sys.argv)</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures"><span class="Apple-converted-space">
</span>File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures"><span class="Apple-converted-space">
</span>raise OSError('Could not find tissue probability maps.\n'</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures">OSError: Could not find tissue probability maps.</span></p>
<p class="p1" style="margin:0px;font:11px Menlo"><span class="s1" style="font-variant-ligatures:no-common-ligatures">Probably something went wrong with the Matlab call or SPM</span></p>
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My participant folder has an "org" folder with the T1.nii and T2.nii in them. </div>
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I have Matlab installed on my computer. I am not sure if it is an error with where SIMNIBS downloads on my computer - it seems to only download under a "user" - as you can see from the screenshot - it is the only application in the application folder. In my
generic application folder - simnibs doesn't show up visually - though when I open it through terminal it does. I am not sure if this is why it cannot find the site-packages within simnibs. I also tried changing the permission of the application (chmod options)
and did not have any success. </div>
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I also tried installing simnibs on another user on my computer and on another Mac computer and got the same error. I have used simnibs before and have never had this error. </div>
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I have tried to fix this over the last few days and watched the tutorial videos - I can't seem to fix the problem. I updated simnibs to the current version. I also uninstalled it and tried installing it again and am having the same issue. This problem has only
occurred using this version. I previously ran 25 head models on the previous version and did not have any issues. </div>
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Attached are all the screen shots of my error messages and the code I am using to run the headmodels. </div>
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mvp1.sh is the script I am using. I tried "headreco all" and headreco all --cat". The headreco_log.html file is also attached. </div>
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I appreciate your time and help!</div>
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Thank you in advance!</div>
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Kind regards, </div>
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Adrianna</div>
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--</div>
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<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">Adrianna Giuffre | PhD Candidate (Neurosciences) | CSEP-CPT</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">University of Calgary</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">Calgary Pediatric Stroke Program</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">Alberta Children’s Hospital</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">28 Oki Drive NW, Calgary, AB, Canada
</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">T3B6A8</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">403-955-2471</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">adrianna.giuffre1@ucalgary.ca</p>
<p class="MsoNormal" style="margin-top:0px; margin-bottom:0px">Program website: <a href="http://www.perinatalstroke.com">
www.perinatalstroke.com</a></p>
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