<pre><font size="4">Hi Jan-Mathijs<br><br>Thanks for you reply, I just figure out where the problem is coming from <br>(and you are totally right about the <i> <a href="http://cfg.name">cfg.name</a> = 'ctf'<font size="4"> :-) </font></i>, completely no sens what I wrote... )<br>
So the problem I had (and I also had some problems while using ft_prepare_headmodel) is coming from the ft_defaults.m, the one from<br>more recent release which is not working for me.... (I always run </font><font size="4"><font size="4">ft_defaults before executing my program<font size="4">s</font></font>)<br>
So I used the one from the 20111024 release</font><br><font size="4">Now, everything is working! <br><br></font><font size="4"><font size="4">I a<font size="4">lso talk to a<font size="4">nother Fi<font size="4">eldtrip user in our lab, and he could<font size="4">n't run the fieldtrip<font size="4"> functions, unless 'adding </font></font></font></font></font></font></font><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4">fieldtrip directory in </font></font></font></font></font></font></font></font></font></font></font>path with subfo<font size="4">l<font size="4">ders' <br>
<font size="4">which create<font size="4">d <font size="4">conflicts with eeglab toolbox...<br><font size="4"><font size="4">I</font>s there actually a pr<font size="4">oblem with the </font></font></font></font></font></font></font></font></font></font></font></font></font></font></font><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4"><font size="4">ft_defaults.m file itself or is it coming from our M<font size="4">atlab version (2012b)? What shou<font size="4">ld we use<font size="4"> inst<font size="4">ead?</font></font></font></font></font></font></font></font></font></font></font></font></font></font></font></font></font><br>
<br><font size="4"><font size="4">Thanks!<br><font size="4">Cheers, </font><br><br><font size="4">Sophie <br><br><br></font></font></font><br>Dear Sophie,
What happens if you don't specify <a href="http://cfg.name">cfg.name</a>? It seems that you don't need the output to be written to a file anyway (since you also specify cfg.write = 'no');
Best,
Jan-Mathijs
On Feb 12, 2013, at 11:46 AM, sophie chen wrote:
><i> Dear Fieldtripers
</i>><i>
</i>><i> I am having some errors when running recent fieldtrip releases while calling ft_volumesegment that I don't have with former fieldtrip version, following what I get:
</i>><i> with fieldtrip fieldtrip-20111024
</i>><i>
</i>><i> cfg = [];
</i>><i> <a href="http://cfg.name">cfg.name</a> = 'ctf';
</i>><i> cfg.output= { 'tpm' };
</i>><i> segmentedmri = ft_volumesegment(cfg, mri);
</i>><i>
</i>><i> Warning: adding D:\SOPHIE\Software\fieldtrip-20111024\external\spm8 toolbox to your Matlab path
</i>><i>
</i>><i> the input is volume data with dimensions [256 256 256]
</i>><i> Converting the coordinate system from ctf to spm
</i>><i> performing the segmentation on the specified volume
</i>><i> segmentedmri =
</i>><i> dim: [256 256 256]
</i>><i> transform: [4x4 double]
</i>><i> coordsys: 'ctf'
</i>><i> unit: 'mm'
</i>><i> gray: [256x256x256 double]
</i>><i> white: [256x256x256 double]
</i>><i> csf: [256x256x256 double]
</i>><i> cfg: [1x1 struct]
</i>><i>
</i>><i> with fieldtrip 'fieldtrip-20121203'
</i>><i>
</i>><i> >> cfg = [];
</i>><i> <a href="http://cfg.name">cfg.name</a> = 'ctf';
</i>><i> cfg.write = 'no';
</i>><i> cfg.output= { 'tpm' };
</i>><i> segmentedmri = ft_volumesegment(cfg, mri);
</i>><i>
</i>><i> Warning: FieldTrip is not yet on your MATLAB path, adding D:\\SOPHIE\\Software\\fieldtrip-20121203(1)\\fieldtrip-20121203
</i>><i> > In ft_defaults at 60
</i>><i> In ft_volumesegment at 130
</i>><i> the input is volume data with dimensions [256 256 256]
</i>><i> Converting the coordinate system from ctf to spm
</i>><i> Rescaling NIFTI: slope = 0.00342945, intercept = 0
</i>><i> Smoothing by 0 & 8mm..
</i>><i> Coarse Affine Registration..
</i>><i> Fine Affine Registration..
</i>><i> Error using ft_write_mri (line 128)
</i>><i> unsupported data format
</i>><i> Error in ft_volumesegment (line 274)
</i>><i> Va = ft_write_mri([<a href="http://cfg.name">cfg.name</a>,'.img'], mri.anatomy, 'transform', mri.transform, 'spmversion', cfg.spmversion);
</i>><i>
</i>><i>
</i>><i> and 'fieldtrip-20130210'
</i>><i>
</i>><i> cfg = [];
</i>><i> <a href="http://cfg.name">cfg.name</a> = 'ctf';
</i>><i> cfg.write = 'no';
</i>><i> cfg.output= { 'tpm' };
</i>><i> segmentedmri = ft_volumesegment(cfg, mri);
</i>><i>
</i>><i> the input is volume data with dimensions [256 256 256]
</i>><i>
</i>><i> Warning: adding D:\SOPHIE\Software\fieldtrip-20130210\fieldtrip-20130210\external\spm8 toolbox to your Matlab path
</i>><i>
</i>><i> Converting the coordinate system from ctf to spm
</i>><i>
</i>><i> Warning: adding D:\SOPHIE\Software\fieldtrip-20130210\fieldtrip-20130210\external\freesurfer toolbox to your Matlab path
</i>><i>
</i>><i> Rescaling NIFTI: slope = 0.00342945, intercept = 0
</i>><i> Smoothing by 0 & 8mm..
</i>><i> Coarse Affine Registration..
</i>><i> Fine Affine Registration..
</i>><i> Warning: could not open ctf.img
</i>><i> > In fileio\private\warning_once at 116
</i>><i> In fileio\private\filetype_check_header at 54
</i>><i> In ft_filetype at 338
</i>><i> In ft_write_mri at 54
</i>><i> In ft_volumesegment at 282
</i>><i> Error using ft_write_mri (line 128)
</i>><i> unsupported data format
</i>><i> Error in ft_volumesegment (line 282)
</i>><i> Va = ft_write_mri([<a href="http://cfg.name">cfg.name</a>,'.img'], mri.anatomy, 'transform', mri.transform, 'spmversion', cfg.spmversion);
</i>><i>
</i>><i> Please help... :-) it's not convenient to switch fieldtrip version while running scripts...
</i>><i> Thanks a lot!
</i>><i>
</i>><i> cheers
</i>><i> Sophie
</i>><i> _______________________________________________
</i>><i> fieldtrip mailing list
</i>><i> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">fieldtrip at donders.ru.nl</a>
</i>><i> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a>
</i>
Jan-Mathijs Schoffelen, MD PhD
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">J.Schoffelen at donders.ru.nl</a>
Telephone: +31-24-3614793</font></pre>