Providing the original images that you enter into SPM5/8 are in the
correct format, then the coordinates that SPM - or any other NIfTI
compliant software - assigns to the voxels should be correct.
Best regards,
-John
On Wed, 2009-10-14 at 16:39 -0400, Steven Liu wrote:
> Dear SPM8 expert:
>
> I have been using SPM2, but just recently I satrted
> using SPM8.
> One thing I feel very confusing here:
>
> In SPM2, if we use spm_defaults to set the defaults,
> then
> defaults.analyze.flip =0, meaning that SPM will never do
> flipping
> operation. So, if we want to flip, we must do it by ourselves
> manually.
> For example, after we convert DICOM epi (GE scanner) data
> into
> Analyze 7.5 format, becasue the original DICOM images use
> Radiological
> convention, if we want to convert them into Neurological
> convention, we can
> simply do it using SPM->Display->flip y (-1) and save them,
> which will
> generate an associated .mat file for each Analyze image file.
> From then,
> we know that we will always use Neurological Convention all
> the time including
> the results.
>
> But in SPM8, what I cannot understand is:
>
> I know that SPM8 uses NIfTI-1 format. So I fist converted my
> Analyze EPI files
> into NIfTI-1 images by using SPM8 to Diaply images -> y flip
> -> save them into NIfTI-1 format.
> After this, I opened the header of one file, I found that the
> value of the first row and first column in
> the .mat matrix is positive, meaning that this is a
> Neuroligical Convention.
> But after I normalize the Neurological-convention EPI images
> into a avg152T1.nii structural template file,
> the normalized EPI become Radiological Convention again. Then
> I found the avg152T1.nii in SPM8
> is actualy Radiological Convention and so I converted this
> file into a Neurological-convention
> file by doing y flip (after that, the first row and first
> column is positive in .mat matrix in the header). Then
> I re-normalize my Neurological-convention EPI files to the
> Neuroligical-convention template file,
> But surprisingly, after this normalization, the EPI files
> become Radiological Convention
> again !!! So, Why?? SPM8 is always using Radiological
> Convention?
>
>
> Steven
>
>
--
John Ashburner <[log in to unmask]>
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