Q: Hi All, I’m trying to align a PET volume to it’s anatomy, and am running into some problems (and could use some help). I just have a couple of questions …

(1) do I need to resample my anatomical volume to match that of the functional volume prior to calling minctracc?

(2) when I try to resample the native MRI to the functional, I usually get an empty volume out. I suspect that this is related to the difference in z-start values, but am unsure how to proceed. The 2 input volumes look like this …

• MRI **
  file: lestat_t1_native.mnc
  image: signed__ short 0 to 4095
  image dimensions: xspace zspace yspace
  dimension name length step start
  -------------- ------ —— -----

   xspace                    176            1     −85.4759
    zspace                    256           −1      113.831
    yspace                    224           −1      144.386

• PET **
  file: pibXmean.mnc
  image: unsigned byte 0 to 255
  image dimensions: zspace yspace xspace
  dimension name length step start
  -------------- ------ —— -----

   zspace                     63       −2.425       −452.7
    yspace                    128      2.05941     −130.772
    xspace                    128      2.05941     −130.772

The mincresample command and the resulting volume looks this …
>>mincresample -verbose -clobber -like pibXmean.mnc lestat_t1_native.mnc lestat_t1_native_rsl.mnc

• resampled empty T1 volume —
  file: lestat_t1_native_rsl.mnc
  image: signed__ short 0 to 4095
  image dimensions: zspace yspace xspace
  dimension name length step start
  -------------- ------ —— -----

   zspace                     63       −2.425       −452.7
    yspace                    128      2.05941     −130.772
    xspace                    128      2.05941     −130.772

(3) does minctracc want both volumes to share the same data type (e.g. byte) or does this not matter?

(4) should I blur the native T1 prior to fitting? … or does minctrac deal with this?
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2008-May/002059.html

A: (1)Nope.
(2) That mincresample call won’t work due to the difference in starts and steps between the two images - you’ll need to compute the transform first and then resample.
(3) This does not matter - though if you need to do mutual information registration, then it will reshape them to unsigned byte automatically.
(4)Probably - especially with those differences in initial position you’ll probably want to use a multiscale algorithm anyway; i.e. first transform with quite blurred data, second transform with less blurring, etc.