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<p>I did get the same message before and after recompiling so it didn't seem to do anything.</p>
<p>I did try and get rid of the .mexa64 but now I get:</p>
<p> </p>
<div>Warning: adding /geode2/home/u060/mattwint/Carbonate/fieldtrip-r10442/external/gifti toolbox to your MATLAB path </div>
<div>Array indices must be positive integers or logical values.</div>
<div><br>
</div>
<div>Error in xml_parser>tag_element (line 227)</div>
<div> xtree{Xparse_count} = element;</div>
<div><br>
</div>
<div>Error in xml_parser>compile (line 199)</div>
<div> frag = tag_element(frag);</div>
<div><br>
</div>
<div>Error in xml_parser (line 134)</div>
<div>tree = compile(tree);</div>
<div><br>
</div>
<div>Error in xmltree (line 41)</div>
<div> tree.tree = xml_parser(varargin{1});</div>
<div><br>
</div>
<div>Error in ft_read_cifti (line 136)</div>
<div>tree = xmltree(xmldata);</div>
<div> <br>
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<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen@donders.ru.nl><br>
<b>Sent:</b> Monday, March 16, 2020 9:49 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> [External] Re: [FieldTrip] Cifti Problem a.k.a. ft_getopt.mexa64 problem</font>
<div> </div>
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<br>
Hi Matt,
<div class=""><br class="">
</div>
<div class="">Strange, typically the mex-files under linux behave relatively well.</div>
<div class=""><br class="">
</div>
<div class="">Are you sure that everything went well, when you recompiled the mex files? The mex-files exist at various locations in the toolbox, for instance, ft_getopt is not only located in fileio/private, but als in private utilities/private forward/private
etc.</div>
<div class="">It could be that you re-compiled something, but that the latest version of the compilation did not end up at the right location.</div>
<div class=""><br class="">
</div>
<div class="">Also, you could try and delete the *.mexa64 version of the file from the location where it causes problems. This leads to fieldtrip falling back to the slower (but hopefully still functional) version of ft_getopt.m</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 15 Mar 2020, at 20:06, Winter, Matthew <<a href="mailto:mattwint@iu.edu" class="">mattwint@iu.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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Hi Jan,<br class="">
</div>
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Thanks for getting back to me. I am working on a linux cluster for Indiana University. the matlab version is 2019. I am typing in:<br class="">
</div>
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<br class="">
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>>ft_read_cifti('100307_MEG_Wrkmem_srcavglcmv_[LM-TIM-0B]_[IT-avg].power.dtseries.nii')<br class="">
</div>
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in response I get: <br class="">
</div>
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<br class="">
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Invalid MEX-file '/geode2/home/u060/mattwint/Carbonate/fieldtrip-r10442/fileio/private/ft_getopt.mexa64':</div>
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/geode2/home/u060/mattwint/Carbonate/fieldtrip-r10442/fileio/private/ft_getopt.mexa64: undefined symbol: mxErrMsgTxt<br class="">
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Error in ft_read_cifti (line 58)</div>
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readdata = ft_getopt(varargin, 'readdata', []); % the default depends on file size, see below<br class="">
</div>
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<br class="">
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I have tried re-configuring the MEX-files, as that was one suggestion, and it didn't change anything. <br class="">
</div>
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If you need more info, let me know and I will do my best to supply it.<br class="">
</div>
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Thank again, I really appreciate any advice. <br class="">
</div>
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Best,<br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
Matt<br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Sunday, March 15, 2020 6:40 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[External] Re: [FieldTrip] Cifti Problem</font>
<div class=""> </div>
</div>
<div class="">
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<br class="">
Hi Matt,
<div class=""><br class="">
</div>
<div class="">Could you be a bit more specific please? What is your operating system and matlab version?</div>
<div class="">What is the exact error message you get, i.e. which mex-file is invalid?</div>
<div class=""><br class="">
</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div class="" style="word-wrap:break-word; line-break:after-white-space">
<div class="" style="word-wrap:break-word; line-break:after-white-space">
<div class="" style="word-wrap:break-word; line-break:after-white-space">
<div class="" style="word-wrap:break-word; line-break:after-white-space">J.M.Schoffelen, MD PhD<br class="">
Associate PI, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space">Physical location: room 00.028</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space">Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
<br class="">
<br class="">
</div>
</div>
</div>
</div>
</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 14 Mar 2020, at 20:07, Winter, Matthew <<a href="mailto:mattwint@iu.edu" class="">mattwint@iu.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
Hi, <br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
<br class="">
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I am trying to read in a cifti file from HCP-MEG data sets. I have been using the ft_read_cifti(pathway) command, but I keep getting the same error: invalid MEX-file.<br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
I am very new to this and am trying to do a very basic connectivity analysis both for a class and to teach myself how to work with these formats. So, any advice on how to fix this error and any other future steps would be greatly appreciated. <br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
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Best,<br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
Matt<br class="">
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<a href="https://doi.org/10.1371/journal.pcbi.1002202" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">https://doi.org/10.1371/journal.pcbi.1002202</a><br class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
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<a href="https://doi.org/10.1371/journal.pcbi.1002202" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">https://doi.org/10.1371/journal.pcbi.1002202</a><br class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); text-decoration:none">
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