[FieldTrip] questions

Robert Oostenveld r.oostenveld at donders.ru.nl
Tue Jan 8 11:06:38 CET 2019

Hi Rathinaswamy

> I have MRIs in DICOM format. I followed the instructions in the tutorial
> which are as follows:
> f1=’/Volumes/FDATA_1/HACO_Project/CT_MRI T1 SPGR/ARS_MRI_T1 SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm’;
> mri = ft_read_mri(f1);
> This threw the following error message.
> SPGR/1.2.840.113619.2.353.4120.14262029.13982.1485259768.788.dcm does not have a series number
> Output argument "vol" (and maybe others) not assigned during call
> to "load_dicom_series."
> Error in ft_read_mri (line 300)
>    [img,transform,hdr,mr_params] =
> load_dicom_series(dcmdir,dcmdir,filename);

This error happens in fieldtrip/external/freesurfer/load_dicom_series.m. The series number is used to determine from the (usually long list of) dicom files which ones belong together.

You could try 
mri = ft_read_mri(filename, ‘dataformat’, ‘dicom_old’)
which uses another low-level reading function. Please look at the code in ft_read_mri, around line 302.

Alternatively, you may be able to use an external tool such as dcm2niix to convert the dicom to nifti.

best regards,

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