[FieldTrip] Problems reading in DICOM

[Markus Butz]

Thanks for your replies and help Robert, Jörn, and Eelke!
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. :-(  
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. ;-) 
 
Thanks again and have a good weekend 
Markus 
  
ps: Sorry for the belated thanks! 
 
 

 
Am 13.03.13, schrieb Robert Oostenveld <r.oostenveld at donders.ru.nl>: 


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> Hi  
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> 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.
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> if the files have no extension, the autodetection fails and you should explicitly specify the format as
>    mri = ft_read_mri('single_file_of_DICOM_series', 'format', 'dicom');
> I now realize that to be a hidden option. I'll get that fixed in the function documentation.
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> 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. 
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> cheers
> Robert
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> On 13 Mar 2013, at 14:22, Jörn M. Horschig wrote:
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> > Hi Markus,
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> > I kept on avoiding these errors by using MRIcron's dcm2nii functionality: http://www.mccauslandcenter.sc.edu/mricro/mricron/index.html
> > But pay attention to the coordinate system when importing it into FieldTrip afterwards, it can be quite a hassle...
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> > Maybe Robert or JM know whether reading in .dcm files is possible, but I have to admit that I never tried ;) 
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> > Best,
> > Jörn
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> > On 3/13/2013 12:11 PM, Markus Butz wrote:
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> > > Dear list, 
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> > > I am experiencing problems reading in external MRI in DICOM format from a CD (doing it the first time though). 
> > > I wanted to do it the new and easy way as described here:
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom
> > > 
> > > 
> > > % read the DICOM files 
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > 
> > > 
> > > 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.
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> > > When I try to open a single file of the *.dcm series I get:
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> > > mri = ft_read_mri('508652C3.dcm');
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> > > ??? Undefined function or variable "hdr".
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> > > Error in ==> ft_read_mri at 216
> > >   hdr     = hdr(keep); 
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> > > Trying to read in a single file of the no extension series I get:
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> > > mri = ft_read_mri('73850486');
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> > > ??? Error using ==> dicominfo at 41
> > > The specified file is not in DICOM format
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> > > 
> > > The Image Processing toolbox V 7.2 is installed and this is fieldtrip-20111101.
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> > > 
> > > Any help appreciated!
> > > 
> > > 
> > > Markus
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> > > 
> > >  
> > > 
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > 
> > 
> > 
> > 
> > -- 
> > 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: jm.horschig at donders.ru.nl
> > Tel:    +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> > 
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> > 
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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