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