Hello,

I've used the command acpcdetect -i anat.nii on my anatomical image, and the outputted anat_RAS.nii came cropped at the top of the head. Is this to be expected? I tried playing with the different options but the image produced is always slightly cropped at the top...
When I load both the anat and anat_RAS in fsleyes both images have the same dim1, dim2 and dim3, but they have different X,Y, Z sizes.

Best regards,
Sam

Originally posted by sam1:
Hi Sam,

Is it possible that anat.nii did not cover the entire head to begin with?   Another possibility is that MSP and AC/PC detection simply failed for this case.  You can check that by looking at the *PPM images which show the detected landmarks and the MSP.   Regarding dimensions, acpcdetect allows you to explicitly specify the output dimensions (both matrix sizes and voxel sizes).  

Babak