Thanks for all the help! We did figure it out now. It was just to use
dcm2nii. Dcm2nii first generated 3d nii images, and then it was just
to convert these 3d images to 4d nii using dcm2nii. The sequence used
is a SSFP sequence under development, so that was probably why we
experienced some problems
Best regards
Hallvard
--------------------------------------------------------
Siterer "Auer, Tibor MD." <[log in to unmask]>:
> Hi,
>
> Have you ever tried dinifti (http://cbi.nyu.edu/software/dinifti.php)?
> I use Ubuntu and it is also available in repos (using e.g. apt-get).
> As far as I experienced it works for me the same way as mri_convert (from
> FreeSurfer); and I have never had any problem.
>
> Best,
>
> Auer, Tibor M.D.
> Biomedizinische NMR Forschungs GmbH
> am Max-Planck Institut für Biophysikalische Chemie
> Am Fassberg 11
> 37077 Göttingen
> Germany
> Phone/Work: +49-(0)551-201-1725
> Phone/Home: +49-(0)551-250-4576
> Mobile: +49-(0)176-8012-7921
> Mail: [log in to unmask]
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Mark Jenkinson
> Sent: Wednesday, March 18, 2009 1:06 PM
> To: [log in to unmask]
> Subject: Re: [FSL] From dicom to nii
>
> Hi,
>
> They don't use the file order for our dicom images, so I guess they
> don't generally.
> However, there are lots of variations of dicom around, depending on
> the manufacturer
> of the scanner and/or the programmer of the sequence. Is it a
> standard sequence on
> a common scanner that you are trying to convert, or something a little
> more unusual?
>
> There maybe people out there who have solved your exact problem if you
> can provide
> a little more info.
>
> All the best,
> Mark
>
>
>
> On 18 Mar 2009, at 10:20, Hallvard Røe Evensmoen wrote:
>
>> Yes I have:) I am not sure exactly what kind of information from the
>> dicom files that these programs use. But based on the problems I
>> get, I suspect that they don`t sort the images based on header info,
>> but instead depend on the sequence that the dicom images are stored
>> in. Do you know anything about that?
>>
>>
>> Hallvard
>>
>> ---------------------------------------------------
>> Siterer Mark Jenkinson <[log in to unmask]>:
>>
>>> Hi,
>>>
>>> We have had good results from using mri_convert (from FreeSurfer)
>>> or dcm2nii (from mricron). Have you tried these?
>>>
>>> All the best,
>>> Mark
>>>
>>> P.S. You can only attach very small files to emails that go to the
>>> whole FSL list, to avoid everyone getting full mailboxes.
>>>
>>>
>>> On 18 Mar 2009, at 09:05, Hallvard Røe Evensmoen wrote:
>>>
>>>> I have tried to convert a series of 3d dicom images into nifti using
>>>> dicom2nii, MRIConverter and LONI debabeler. The best I get is all
>>>> the
>>>> slices from the different volumes added together with dim3=1 (image
>>>> attached). Anyone got a better suggestion than writing a scipt
>>>> that first
>>>> uses fslmerge to merge the 32 slices along the z axis to get the
>>>> volumes and
>>>> finally use fslmerge to merge the volumes in time.
>>>>
>>>>
>>>> Yours sincerely
>>>>
>>>> Hallvard Røe Evensmoen
>>>>
>>
>
>
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