[Camino-users] Expanded NIfTI support since r1175

[Philip A Cook]

Hi,

Most apps should now support output to an nii file, and should accept nii input. I have tested some common use cases but it is still fairly new code so please let me know if there are any problems. Backwards compatibility is preserved for people handling raw data.

Example:

  track -inputfile dwi4D.nii.gz

  dtfit dwi4D.nii.gz schemefile | fa -header dwi4D.nii.gz -outputfile fa.nii.gz

Using large nii input files will require more memory as the entire file is read in and re-ordered on the fly, but it can be more convenient.


Vector data can be written to a 4D NIFTI file. One possibly confusing thing, if you do

  dtfit dwi4D.nii.gz schemefile -outputfile dt.nii.gz

You will get the 8-component Camino output in nii vector form, not a DT image. To get a DT image, do

    dtfit dwi4D.nii.gz schemefile | dt2nii -header dwi4D.nii.gz -outputroot dt_

To convert vector data to 3D nii images, call voxel2image.


Vector data can also be read, eg

  modelfit -model pospos ... -outputfile twoDT.nii.gz

  dteig -inputfile twoDT.nii.gz -inputmodel multitensor > eig.Bdouble



There is one special case, allowing input of tensors when DT input is expected. 

Example:

  track -inputmodel dt -inputfile dtitk_dt.nii.gz ...

will read a NIFTI_SYMMATRIX correctly, though obviously there's no exit code etc. This is therefore equivalent to

  nii2dt -inputfile dtitk_dt.nii.gz |  track -inputmodel dt ...

Meanwhile, 

  dtfit data.nii.gz scheme -outputfile caminodt.nii.gz

  dteig -inputfile caminodt.nii.gz -outputfile eig.nii.gz 

will read the standard Camino output (8 components) and produce a NIFTI output.

image2voxel will convert any of these files back to voxel order if needed.