At one point the afni converter "cardinalized" the qform matrix, ie, if
the matrix represented an oblique slice prescription, it would make it
non-oblique. This still preserves the basic orientation (ie, left is
still left and right is still right), but you end up losing scanner
coordinates which can be quite useful. I know Bob is aware of the issue,
but I don't know whether it is fixed or not. Anyone know?
doug
Daniel Glen wrote:
> Actually to3d can convert the DICOM files directly to NIFTI without
> using the 3dAFNItoNIFTI program by simply specifying the -prefix
> option to end with .nii. You can use the Dimon program with the -
> GERT_Reco and -dicom_org options to create a script that contains an
> appropriate to3d command and to generate a list of files to convert.
> Dimon can figure out file numbering issues caused by naming problems,
> duplicate or missing data.
>
> Dimon -infile_prefix s8912345/i -dicom_org -GERT_Reco -quit
>
> Daniel Glen
>
> On Oct 10, 2007, at 4:08 PM, Sheyna Gifford wrote:
>
>> Carlos-
>>
>> I highly recommend using Afni's 3dAFNItoNIFTI call. Works like a
>> charm.
>> Afni is free and runs on basically any platform. The only hitch: the
>> data
>> has to be in Afni format first. The command to convert dicoms into Afni
>> briks is called to3d.
>>
>> See the docs. It's simple and easy once you've tried it once or twice.
>>
>> http://afni.nimh.nih.gov/afni/doc/edu/afni02_to3d
>> http://afni.nimh.nih.gov/pub/dist/doc/program_help/to3d.html
>>
>> - seg
>>
>> On 10/10/07 2:20 PM, "Carlos Faraco" <[log in to unmask]> wrote:
>>
>>> I have actually tried the DICOM converter from SPM5 and it says it
>>> cannot
>>> determine what order the images is in and will just guess. Thank
>>> you, and
>>> everyone else, for the suggestions. I will try them.
>>>
>>> -Carlos
>>
>>
>> --
>>
>> Sheyna Gifford
>> Research Specialist
>> Magnetic Resonance Imaging Research Facility
>> Brown University
>> Box G-L
>> 401-863-6513
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[log in to unmask]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
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