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<div class="moz-cite-prefix">Hi Markus,<br>
<br>
I kept on avoiding these errors by using MRIcron's dcm2nii
functionality:
<a class="moz-txt-link-freetext" href="http://www.mccauslandcenter.sc.edu/mricro/mricron/index.html">http://www.mccauslandcenter.sc.edu/mricro/mricron/index.html</a><br>
But pay attention to the coordinate system when importing it into
FieldTrip afterwards, it can be quite a hassle...<br>
<br>
Maybe Robert or JM know whether reading in .dcm files is possible,
but I have to admit that I never tried ;) <br>
<br>
Best,<br>
Jörn<br>
<br>
On 3/13/2013 12:11 PM, Markus Butz wrote:<br>
</div>
<blockquote cite="mid:74308a1f1ca78.51405ed9@uni-duesseldorf.de"
type="cite">
<div>
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<div style="min-height: 1em; ">Dear list, </div>
<div><br>
</div>
<div style="min-height: 1em; ">I am experiencing problems
reading in external MRI in DICOM format from a CD (doing it
the first time though). </div>
<div style="min-height: 1em; ">I wanted to do it the new and
easy way as described here:</div>
<div style="min-height: 1em; "><a moz-do-not-send="true"
href="http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom"
target="1">http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom</a></div>
<div><br>
</div>
<div style="min-height: 1em; "><span class="co1">% read the <span
class="search_hit">DICOM</span> files </span><br>
mri = ft_read_mri<span class="br0">(</span><span class="co2">'single_file_of_DICOM_series.IMA'</span><span
class="br0">)</span>;</div>
<div><br>
</div>
<div style="min-height: 1em; ">However, I have no single
slices with extension *.ima but one dataset with the
extension *.dcm and the other dataset with no extension for
the single slice files. I am also not sure where to copy the
DICOMDIR file.</div>
<div><br>
</div>
<div style="min-height: 1em; ">When I try to open a single
file of the *.dcm series I get:</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">mri =
ft_read_mri('508652C3.dcm');</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">??? Undefined function or
variable "hdr".</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">Error in ==> ft_read_mri at
216</div>
<div style="min-height: 1em; "> hdr = hdr(keep); </div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">Trying to read in a single file
of the no extension series I get:</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">mri = ft_read_mri('73850486');</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">??? Error using ==>
dicominfo at 41</div>
<div style="min-height: 1em; ">The specified file is not in
DICOM format</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">The Image Processing toolbox V
7.2 is installed and this is fieldtrip-20111101.</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">Any help appreciated!</div>
<div style="min-height: 1em; "><br>
</div>
<div style="min-height: 1em; ">Markus</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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