<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body>
<p>Hi Adrianna,</p>
<p><br>
</p>
<p>thank you for providing the detailed information. Which OS
version do you use? <br>
</p>
<p>We will see whether we can replicate it on our test Mac. In case
it runs fine here, I would likely suggest a zoom meeting so that
we can have a look at the issue together. </p>
<p> <br>
</p>
<p>Best regards,</p>
<p>Axel</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 11/18/2020 7:31 PM, Adrianna Giuffre
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:YTBPR01MB362913145A53297F8C8C6AAFADE10@YTBPR01MB3629.CANPRD01.PROD.OUTLOOK.COM">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;}</style>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Hello</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
My name is Adrianna Giuffre - I am a PhD candidate at the
University of Calgary. </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
I am using SimNIBS for a current modelling project. </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
I am having the problems running new head models.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<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>
<br>
</div>
<div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
My participant folder has an "org" folder with the T1.nii and
T2.nii in them. </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Attached are all the screen shots of my error messages and the
code I am using to run the headmodels. </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
I appreciate your time and help!</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Thank you in advance!</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Kind regards, </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Adrianna</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
--</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div>
<div id="divtagdefaultwrapper" dir="ltr"
style="font-size:12pt; color:#000000;
font-family:Calibri,Helvetica,sans-serif">
<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"><a class="moz-txt-link-abbreviated" href="mailto:adrianna.giuffre1@ucalgary.ca">adrianna.giuffre1@ucalgary.ca</a></p>
<p class="MsoNormal" style="margin-top:0px;
margin-bottom:0px">Program website: <a
href="http://www.perinatalstroke.com"
moz-do-not-send="true">
www.perinatalstroke.com</a></p>
<p class="MsoNormal" style="margin-top:0px;
margin-bottom:0px"> </p>
<br>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Simnibs-discuss mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Simnibs-discuss@drcmr.dk">Simnibs-discuss@drcmr.dk</a>
<a class="moz-txt-link-freetext" href="https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
<a class="moz-txt-link-abbreviated" href="http://www.drcmr.dk">www.drcmr.dk</a>
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
<a class="moz-txt-link-freetext" href="http://www.healthtech.dtu.dk/">http://www.healthtech.dtu.dk/</a></pre>
</body>
</html>