HI 
I am trying to use PIL transformation in FSL format to reorient masks in ACPC RAS space.
Applying the PIL transform to the native T1 image (acpcdetect input) doesn't give the same result as the acpcdetect output (t1_RAS.nii).

I tried to use the ART reslice program to apply the mrx file to the native T1 but the result is different from acpcdetect output (and different from the output of flirt). It is also strange that when using relisce with the output mrx transform from yuki (with the same t1 image as input), the output is different that when using the transform from acpcdetect (image is completely flipped).
I also tried converting the initial T1 to PIL orientation (with fslswapdim) before applying PIL transformation but there is still a difference between the output of flirt and the output of acpcdetect (t1_RAS.nii)
Is there a simple method to apply the PIL transform from ACPCdetect to masks using flirt (or another program) ?
The only workaround I found so far is to comput a new transform with flirt between the native T1 image and the output of acpcdetect (t1_RAS.nii)
Best regards
Matthieu