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
>>>
>>>  
>>>   
>>>       
>
>
>