Hi,
Development sequences are tricky in this way.
It really matters what information gets written into the dicom files.
Glad you found a solution.
All the best,
Mark
Hallvard Røe Evensmoen wrote:
> 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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