Command (FS v4.1.0) was just: mri_convert --out_orientation input.nii output.nii
Then, loading both input.nii and output.nii into tkmedit, it is clear that the voxel values at the same cursor location do not match. (output.nii is clearly smoother, consistent with it being interpolated). thanks, -MH On Fri, 2010-02-05 at 14:30 -0500, Douglas N Greve wrote: > > Michael Harms wrote: > > 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). > > > Yes, it is. It is actually only in the dev version. > > Also, can you please clarify what do you mean when you said that -- > > out_orientation should not resample? > > > It should only change the geometry in the header, not the pixel values. > What's your cmd? > > 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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