[Camino-users] some problem with the command of 'reorient'

[Alexander, Daniel]

Hi,

The reorient man page explains how to use it with non-linear transformations: http://cmic.cs.ucl.ac.uk/camino//index.php?n=Man.Reorient.

Danny


On 9 Jan 2015, at 07:32, 穆俊娅 <mjy0312 at 163.com<mailto:mjy0312 at 163.com>> wrote:

Dear all,
      In the “DWI Registration and Spatial Normalization of DTI” of Camino Tutorials, there is the case study shows how to combine FSL’s flirt program with Camino’s tensor reorientation to perform spatial normalization of diffusion tensor images (using PPD algorithm).
      In that example, the Camino uses the following line to warp the tensor image,
      flirt -in Control1_DT_Comp${i}.img -applyxfm -init C1C3_Affine.txt -out Control1_DT_Comp${i}_SN.img -ref Control3_FA.img -interp nearestneighbour
      and then uses the following line to reorient the tensors:
      reorient -trans C1C3_Affine.txt < Control1_DT_SNNR.Bdouble > Control1_DT_SNPPD.Bdouble
 Here is my question:
Note that reorient will also work with non-linear warps produced by FSL's non-linear registration program fnirt. How we do that?
In my idea, we need to warp the tensor image by using fnirt. As similar to the above command line in flirt, what is the command of fnirt?
After that, to perform reorientation for a non-linear transformation, we then need to use this command?

        reorient -trans Warp.nii -datadims 128 128 60 -voxeldims 1.7 1.7 2.3 < SubjectA_DT_Warp.Bdouble > SubjectA_DT_WarpPPD.Bdouble
I’m looking forward to your response. Feel free to contact me anytime.
       Sincerely,
       mirabelle


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