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FSL  March 2009

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Subject:

Re: From dicom to nii

From:

"Auer, Tibor MD." <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 18 Mar 2009 14:10:21 +0100

Content-Type:

text/plain

Parts/Attachments:

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text/plain (92 lines)

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 fr Biophysikalische Chemie 
Am Fassberg 11
37077 Gttingen
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 Re 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 Re Evensmoen
>>>
>

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