Hi,
The page also contains a list of alternative methods at the bottom.
You might want to try mri_convert too (part of FreeSurfer) which is
a command-line tool and should manage to do OK.
I can't really comment in more detail on the arrangement of your
files, but it is common to have lots of files around the place in dicom.
All the best,
Mark
On 14 May 2007, at 11:37, Alle Meije Wink wrote:
> Thanks, Mark. I had a look at the link on that page (ie pointing to
> DCM2NII by Chris Rorden). Two things put me off a little bit:
>
> - All the warnings at the top of the site
> - The fact that all the examples are all volumes already
>
> Is there any manual on non-volume DICOM data?
>
> The most difficult/labour-intensive step here seems to be putting
> all the slice-images into volumes. I wondered if there is a tool to
> automate that. Less work, but also: less error prone!
>
> Some dicom servers (or very kind people who run/maintain those
> servers) provide a script called pvconv.pl which seems to do the
> job better than anything else. It is not on my CDs though...
>
> Cheers
> Alle Meije
>
> Mark Jenkinson wrote:
>> Hi,
>> Look at the link in:
>> http://www.fmrib.ox.ac.uk/fslfaq/#general_format
>> All the best,
>> Mark
>> On 14 May 2007, at 10:31, Alle Meije Wink wrote:
>>> Hi all,
>>>
>>> I have got a set of MR files on CD's which are in DICOM format. I
>>> would like to convert them to NIFTI volumes.
>>>
>>> The problem is that instead of being stored as volumes, different
>>> slices seem to be in different files (even different
>>> directories!). The only way that I can view them is with the
>>> DICOM viewer on the CD's and with ImageJ.
>>>
>>> Is it possible to convert DICOM images from that directory
>>> structure to nice 3D (or 4D) NifTI files?
>>>
>>> If there is a command-line option (so that it is scriptable for
>>> the whole CD) which leaves all the patient/scan info in (I can
>>> remove that once the images are in a normal format) then that
>>> would be great.
>>>
>>> I reckon this has been done before (sorry for douoble-posting),
>>> lots of people get their data on CD. Anybody know how to do this?
>>>
>>> Many thanks!
>>> Alle Meije Wink
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