[FieldTrip] How to read .dicom format using FT_READ_MRI

[Cristiano Micheli]

Hi Ying and Stan,
I had the same problem, and I solved it in a 'quick and dirty' way by
changing the name of the first image of the dicom series (i.e. substituting
the dots with underscores). It may help to change/add the extension of the
first file too .

Best of luck!

 Cris


On Fri, Jan 16, 2015 at 9:43 AM, Pelt, S. van (Stan) <
stan.vanpelt at donders.ru.nl> wrote:

>  Dear Ying,
>
>
>
> As far as I understand, Fieldtrip can read in the entire series of
> dicom-files by just specifying the first file name of the series, just like
> you did. However, for this it is required that the series number is clear
> in each file name, e.g. MRI_S01_MEG.0001.0001.IMA,
> MRI_S01_MEG.0001.0002.IMA, etc. I suppose that is not clear in your dicom
> file names.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Ying Li
> *Sent:* woensdag 14 januari 2015 20:05
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] How to read .dicom format using FT_READ_MRI
>
>
>
> Dear all,
>
>
>
> I'm trying to load MRI into matlab. The MRI data I have is a series of
> .dicom files (~250 frames, "IMG1"~"IMG250").  I'm wondering how to specify
> the input parameter for the function "ft_read_mri". Since I have 250 files,
> which file should I use for the input?
>
>
>
> If I only use the first file "IMG1", for example mri =
> ft_read_mri('IMG1');  Then I will get the following error:
>
>
>
> Warning: Not enough data imported.  Attempted to read 3053459760 bytes at
> position 2953.  Only read 534544.
>
> ERROR: IMG1 does not have a series number
>
> Error in load_dicom_series (line 42)
>
> if(nargin < 1 | nargin > 3)
>
>
>
> Output argument "vol" (and maybe others) not assigned during call to
>
>
> "XX\fieldtrip_20140518\external\freesurfer\load_dicom_series.m>load_dicom_series".
>
>
>
> Error in ft_read_mri (line 287)
>
>   [img,transform,hdr,mr_params] =
> load_dicom_series(dcmdir,dcmdir,filename);
>
>
>
> I'll appreciate your reply a lot!
>
>
>
> Best,
>
>
>
> Ying
>
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