[FieldTrip] Problems reading in DICOM

["Jörn M. Horschig"]

Hi Markus,

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...

Maybe Robert or JM know whether reading in .dcm files is possible, but I 
have to admit that I never tried ;)

Best,
Jörn

On 3/13/2013 12:11 PM, Markus Butz wrote:
> Dear list,
>
> 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.
>
> When I try to open a single file of the *.dcm series I get:
>
> mri = ft_read_mri('508652C3.dcm');
>
> ??? Undefined function or variable "hdr".
>
> Error in ==> ft_read_mri at 216
>   hdr     = hdr(keep);
>
> Trying to read in a single file of the no extension series I get:
>
> mri = ft_read_mri('73850486');
>
> ??? Error using ==> dicominfo at 41
> The specified file is not in DICOM format
>
> The Image Processing toolbox V 7.2 is installed and this is 
> fieldtrip-20111101.
>
> Any help appreciated!
>
> Markus
>
>
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> fieldtrip at donders.ru.nl
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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

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
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Visiting address:
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NL-6525 EN Nijmegen
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