The oblique transformation matrix is computed from the DICOM header
and kept now. The matrix is stored in the AFNI header or in the sform
fields of a NIFTI file. The transformation matrix can be applied to
files to either "oblique" or "deoblique" a dataset using 3dWarp.
Otherwise, the cardinal matrix is used in AFNI processing and
display. This web page discusses how to process oblique datasets with
AFNI.
http://afni.nimh.nih.gov/sscc/dglen/Obliquity
Daniel
On Oct 10, 2007, at 4:45 PM, Doug Greve wrote:
> 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:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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