[Mrtrix-discussion] nifti format

[romain valabregue]

Hello,

I have some question nifti file produce by mrtrix

_depending on the data type I can not see file in other nifti viewer 
(fslview or spm)
for instance (  Data type:         bitwise)
I guess I can test different output type with mrconvert but I can't find 
on the docs
which string to give to the  -datatype option


_A second point is about the 2 orientation matrix from the nifti header
The sform is correct, but the qform just set an identity orientation 
(with the voxel size)
why not to set both orientation to the same value ?
I am not sure if it is specify in the nifti definition which orientation 
to use first, but I would set both orientation identical ...

_A last point: I have notice that when nifti file are created (based on 
other nifti file) there is a change of the nifti orientation in the header :
I have orientation with negative pixel size but ater mrconvert it will 
be change with positive valu
 for instance with a sform
-1.71875 0 0 110 0 1.39752 -1.16425 -33.0028 -1.71875e-16 1.00052 1.6262 
-140.284 0 0 0 1
but file produce by mrconvert will then have always positive voxel size
1.71875 0 0  -108.281 -0 1.39752  -1.16425 -33.0028 1.71875e-16 1.00052 
1.6262 -140.284 0 0 0 1

Why not to keep the original nifti header orientation (with both sform 
and qform set) ... ?
I do not realy understand why this change and I wonder if this imply a 
reordening of the data matrix

Many thanks

Romain