Hi Doug,
Is --reorder4 a new feature in one of the more recent releases?
(Currently, I'm using mri_convert from v4.1.0, and I don't see a --
reorder4 flag).
Also, can you please clarify what do you mean when you said that --
out_orientation should not resample?
If I take an nii file with this transform:
Orientation : PSR
Primary Slice Direction: sagittal
voxel to ras transform:
-0.0229 -0.0300 1.1991 -88.7736
-0.9978 0.0634 -0.0251 144.1823
0.0628 0.9975 0.0377 -139.2478
0.0000 0.0000 0.0000 1.0000
and run it through "mri_convert --out_orientation LAS input.nii
output.nii", then mri_convert spits out the following:
Setting output orientation to LAS
Reslicing using trilinear interpolation
And the output.nii has this transform:
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.0000 0.0000 0.0000 120.5695
0.0000 1.0000 0.0000 -97.4406
0.0000 -0.0000 1.2000 -97.0175
0.0000 0.0000 0.0000 1.0000
That is, both the "Reslicing using trilinear interpolation" comment and
the xforms themselves appear to indicate that resampling was performed.
thanks for clarifying,
-MH
On Fri, 2010-02-05 at 14:03 -0500, Douglas N Greve wrote:
> Sorry, I don't have anything that will reorder and change the geometry
> to be correct. You might be able to do it with --reorder4 (and not
> --reorder) in combination with --out_orientation. --out_orientation
> should not resample.
>
> doug
>
> Michael Harms wrote:
> > Hello Doug,
> > Is it possible using mri_convert to just reorder the way in which the
> > data is stored, without any resampling of the actual voxel values?
> >
> > i.e., I have Siemen's MPRAGE DICOMs, and if run mri_convert, I get a
> > default "PIL" orientation. I would like to just reorder the way in
> > which the data is stored, to get a "LAS" orientation instead.
> >
> > I tried using "--out_orientation LAS", but that does a resampling
> > (interpolation) such that the resulting xform has strictly 0's on the
> > off-diagonal. And reading the mri_convert help, it clearly states that
> > the --out_orientation flag is to be used when the input orientation is
> > WRONG, which is not the case here (since I presume that the input
> > orientation is correctly read out of the DICOMs).
> >
> > I tried "--reorder 2 1 3", to see what effect that has on a file already
> > in nii format, but I got the message: in nii format, but I got the
> > message:
> > reordering axes...
> > MRIreorder: incorrect dst width
> > error reordering axes
> >
> > I've checked the archives, and read through the mri_convert help, but
> > just can't seem to figure out if reordering from one orientation to
> > another (without resampling) is possible using mri_convert.
> >
> > thanks,
> > -MH
> >
> >
> >
>
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