help > RE: cropped anatomical image after acpcdetect
Dec 17, 2019  08:12 AM | Babak Ardekani
RE: cropped anatomical image after acpcdetect
Originally posted by sam1:

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,

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).  


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sam1 Dec 17, 2019
RE: cropped anatomical image after acpcdetect
Babak Ardekani Dec 17, 2019