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<DIV>Thanks for your replies and help Robert, Jörn, and Eelke!</DIV><DIV>Finally it worked out, but the problem was rather on my side, as there where several series of different MRTs scans in one folder of which some did not work, some worked out strange as they had just some files (16-26), and some worked fine. Unfortunately I tried most intensively on the subject who came with no correct series at all. :-( </DIV><DIV>To be fair, all the files appeared exactlty the same, but ft_read_mri is luckily mentioning which series it works on and how many files it include, which finally made me wonder. ;-) </DIV><DIV> </DIV><DIV>Thanks again and have a good weekend </DIV><DIV>Markus </DIV><DIV>
<DIV>ps: Sorry for the belated thanks! </DIV><DIV> </DIV><DIV> </DIV></DIV> </DIV><SPAN>Am 13.03.13, schrieb <B class=name>Robert Oostenveld </B><r.oostenveld@donders.ru.nl>:</SPAN> </DIV></DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:985C7F60-4B5F-4E16-B504-437C9095CBEF@donders.ru.nl type="cite">
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<DIV><br /></DIV><DIV>DICOM files come with different extensions. I guess it depends on the scanner (Siemens/Philips/...). But the file format should be the same as it is a standard format, so the extension should not matter. The fileio/ft_filetype.m function detects both dcm and ima files as dicom.</DIV><DIV><br /></DIV><DIV>
<DIV>if the files have no extension, the autodetection fails and you should explicitly specify the format as</DIV><DIV> mri = ft_read_mri<SPAN class=br0>(</SPAN><SPAN class=co2>'single_file_of_DICOM_series', 'format', 'dicom'</SPAN><SPAN class=br0>);</SPAN></DIV><DIV><SPAN class=br0>I now realize that to be a hidden option. I'll get that fixed in the function documentation.</SPAN></DIV><DIV><br /></DIV><DIV>
<DIV></DIV></DIV></DIV><DIV>I recommend that you specify a filename from somewhere in the middle of the stack of files. There are often a few localizer scans in the same directory, and these (due to the sorting of the file names) tend to end up at the beginning or end of the (alphabetical) directory listing. </DIV><DIV><br /></DIV><DIV>cheers</DIV><DIV>Robert</DIV><DIV>
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<DIV>On 13 Mar 2013, at 14:22, Jörn M. Horschig wrote:</DIV><BR class=Apple-interchange-newline>
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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" target=1 >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">
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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 href="http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom" target=1 moz-do-not-send="true">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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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
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