<div dir="ltr">Glad to see it worked, Tom. Full support for SPM12 has only recently been completed, with JM laying the last hand on ft_volumenormalization a couple of weeks ago. Therefore, the issue identified by you might be a missing link that needs to be created still. Do you think you can you propose your solution on github, for further joint discussion and implementation? </div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 10, 2018 at 10:42 AM, Tom Marshall <span dir="ltr"><<a href="mailto:tom.marshall@psy.ox.ac.uk" target="_blank">tom.marshall@psy.ox.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="auto">
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hi Arjen and JM,<br>
<br>
Arjen - thanks for the golden tip! <br>
<br>
As suggested, I explicitly added the SPM12 toolbox and called it in the cfg.<br>
<br>
<i>[status] = ft_hastoolbox('SPM12', 1, 0);<br>
<br>
cfg = [];<br>
cfg.grid.warpmni = 'yes';<br>
cfg.grid.template = template_grid;<br>
cfg.grid.nonlinear = 'yes'; % use non-linear normalization<br>
cfg.spmversion = 'SPM12';<br>
cfg.mri = mri;<br>
sourcemodel = ft_prepare_sourcemodel(cfg);<br>
<br>
</i>However, this didn't totally solve the problem. At one point in ft_prepare_sourcemodel (line 636) ft_volumenormalise is called with a new cfg ('tmpcfg'). The choice to use SPM12 doesn't propagate to tmpcfg so fieldtrip adds SPM8 anyway when it calls ft_volumenormalise.<br>
<br>
I fixed this by adding the following to ft_prepare_sourcemodel at line 633...<br>
<br>
<i>tmpcfg.spmversion = cfg.spmversion;<br>
</i><br>
...and voila! A nice warped source model :)<br>
<br>
Should I file this as a bug?<br>
<br>
Best and thanks for the help,<br>
Tom<br>
<i></i><i></i><br>
<i></i>
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div id="m_4847391127750723789divRpF497203" style="direction:ltr"><font size="2" face="Tahoma" color="#000000"><b>From:</b> <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.<wbr>nl</a> [<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.<wbr>nl</a>] on behalf of Arjen Stolk [<a href="mailto:a.stolk8@gmail.com" target="_blank">a.stolk8@gmail.com</a>]<br>
<b>Sent:</b> 10 January 2018 16:16<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] error in ft_prepare_headmodel<br>
</font><br>
</div><div><div class="h5">
<div></div>
<div>
<div></div>
<div>Hi Tom, </div>
<div><br>
</div>
<div>As another work around, you could try using spm12 functionality. cfg.spmversion = ‘spm12’ if the function supports it, or by manually putting it on the path with ft_hastoolbox. There may be differences in the algorithm/outcome between versions, so you
may want to be consistent in its use across subjects.</div>
<div><br>
</div>
<div>Best,</div>
<div>Arjen</div>
<div><br>
On Jan 10, 2018, at 12:36 AM, Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>Dear Tom,
<div><br>
</div>
<div>To me, this looks like a platform/MATLAB version specific issue with the compiled mex-files. Anecdotally, MATLAB2017a on a Mac suffers from not knowing to handle the precompiled stuff that comes with FieldTrip/SPM. Either you could use a lower
matlab version (e.g. 2016b, which as far as I know does not suffer from this), or you could try and recompile the affected mex-files from the original c-code with the matlab mex-command. See <a href="http://bit.ly/2DeuNlX" target="_blank">http://bit.ly/2DeuNlX</a> for
more info.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div>JM</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 9 Jan 2018, at 17:27, Tom Marshall <<a href="mailto:tom.marshall@psy.ox.ac.uk" target="_blank">tom.marshall@psy.ox.ac.uk</a>> wrote:</div>
<br class="m_4847391127750723789Apple-interchange-newline">
<div>
<div style="font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;direction:ltr;font-family:Tahoma;font-size:10pt">
Howdy 'Trippers,<br>
<br>
I got a weird error when trying to create a template headmodel using ft_prepare_headmodel (basically just following the steps in the tutorial 'Creating a sourcemodel for source-reconstruction of MEG or EEG data').<br>
<br>
After loading and segmenting the template brain I called ft_prepare_headmodel using the suggested parameters.<br>
<br>
<i>cfg = [];<br>
cfg.method = 'singleshell';<br>
template_headmodel = ft_prepare_headmodel(cfg, template_seg);</i><br>
<br>
This gave the following error.<br>
<br>
<i>Error using ft_notification (line 314)<br>
please specificy cfg.tissue and pass an appropriate segmented MRI as input data<br>
<br>
Error in ft_error (line 39)<br>
ft_notification(varargin{:});<br>
<br>
Error in ft_prepare_headmodel (line 354)<br>
ft_error('please specificy cfg.tissue and pass an appropriate segmented<br>
MRI as input data')</i><br>
<br>
So I added cfg.tissue...<br>
<br>
<i>cfg = [];<br>
cfg.method = 'singleshell';<br>
cfg.tissue = 'brain';<br>
template_headmodel = ft_prepare_headmodel(cfg, template_seg);</i><br>
<br>
...and this upset fieldtrip. After printing<span class="m_4847391127750723789Apple-converted-space"> </span><i>'smoothing brain with a 5-voxel FWHM kernel'</i>, it hung for 10-15 minutes, then threw an error with lots of 'Missing symbol' statements (see below - there are
a few hundred more, I just copypasted the last two).<br>
<br>
<i>Missing symbol '_vm_allocate' required by<br>
'/usr/lib/closure/libclosured.<wbr>dylib->/usr/lib/system/<wbr>libdyld.dylib->/usr/lib/<wbr>system/libsystem_platform.<wbr>dylib->/usr/lib/system/<wbr>libsystem_pthread.dylib->/usr/<wbr>lib/system/libcache.dylib->/<wbr>usr/lib/libgcc_s.1.dylib->/<wbr>Users/marshall/Documents/<wbr>MATLAB/fieldtrip-20170726/<wbr>external/spm8/spm_conv_vol.<wbr>mexmaci64'<br>
Missing symbol '_vm_deallocate' required by<br>
'/usr/lib/closure/libclosured.<wbr>dylib->/usr/lib/system/<wbr>libdyld.dylib->/usr/lib/<wbr>system/libsystem_platform.<wbr>dylib->/usr/lib/system/<wbr>libsystem_pthread.dylib->/usr/<wbr>lib/system/libcache.dylib->/<wbr>usr/lib/libgcc_s.1.dylib->/<wbr>Users/marshall/Documents/<wbr>MATLAB/fieldtrip-20170726/<wbr>external/spm8/spm_conv_vol.<wbr>mexmaci64'.<br>
<br>
Error in spm_smooth>smooth1 (line 105)<br>
spm_conv_vol(P,Q,x,y,z,-[i,j,<wbr>k]);<br>
<br>
Error in spm_smooth (line 40)<br>
smooth1(P,Q,s,dtype);<br>
<br>
Error in volumesmooth (line 18)<br>
spm_smooth(output, output, fwhm);<br>
<br>
Error in ft_datatype_segmentation (line 229)<br>
brain = volumesmooth(brain, smooth, 'brain');<br>
<br>
Error in prepare_mesh_segmentation (line 95)<br>
mri = ft_datatype_segmentation(mri, 'segmentationstyle', 'probabilistic',<br>
'hasbrain', 'yes');<br>
<br>
Error in ft_prepare_mesh (line 147)<br>
bnd = prepare_mesh_segmentation(cfg, mri);<br>
<br>
Error in ft_prepare_headmodel (line 337)<br>
geometry = ft_prepare_mesh(tmpcfg, data);<br>
</i><br>
It seems like the problem is somewhere deep down in spm commands that fieldtrip is calling, so maybe nobody has a clue. I'm hoping somebody has seen this before and knows of a fix...<br>
<br>
In case it's relevant: I'm running fieldtrip-20170726 in matlab R2017a on a mac.<br>
<br>
And ideas?<br>
<br>
Best,<br>
Tom<br>
<i></i></div>
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">______________________________<wbr>_________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">fieldtrip
mailing list</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<a href="mailto:fieldtrip@donders.ru.nl" style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">fieldtrip@donders.ru.nl</a><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a></div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div><span>______________________________<wbr>_________________</span><br>
<span>fieldtrip mailing list</span><br>
<span><a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a></span><br>
<span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a></span></div>
</blockquote>
</div>
</div></div></div>
</div>
</div>
<br>______________________________<wbr>_________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a><br></blockquote></div><br></div>