Hi Usman

you may have to repost this question in a few days when Doug is back.

cheers Bruce On Tue, 10 Jul 2012, Usman Khan wrote:

Hi Martin, Thanks for the quick reply. I tried the following commands, but it looks like the volumes are still out of line. Is there something I am missing?

to get from hc_subfield --> nu.mgz --> t1_cbv #register and create transforms

1. mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final

xfm_hcsubfield_to_nu.dat --regheader 2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta xfm_nu_to_t1.lta --satit

#convert output from (1) from reg-final.dat to .lta 3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg xfm_hcsubfield_to_nu.dat --ltaout test.lta 4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta final.lta

#apply lta file, using t1_cbv as target and hc_subfield as --mov file 5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg final.lta --out test.mgz

On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Usman,

  you need to convert the reg to lta (using tkregister2) and then
  you can
  use mri_concatenate_lta .

  Cheers, Martin



  On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote:
  > Hi FreeSurfer,
  > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted
  > (0.682x0.682x3mm) image used for CBV mapping. We have run FS,
  with
  > hippocampal subfields on the MPRAGE and would now like to
  transform
  > the posterior probability maps to the T1-weighted CBV space.
  >
  >
  > I have been using
  > 1) mri_vol2vol with --regheader to map the posterior_*
  subfield files
  > to nu.mgz space
  > 2) mri_robust_register to coregister the nu.mgz file to the
  > T1-weighted CBV image
  >
  >
  > Is there any way to combine the .reg and .lta files from (1)
  and (2)
  > to transform the subfield posterior probability maps directly
  from
  > their 0.5mm^3 space to the T1-weighted CBV space? I have been
  > reluctant to create an intermediate volume between steps 1 and
  2, as
  > resampling the subfield probability maps into 1x1x1mm nu.mgz
  space
  > will result in loss of resolution to the 0.68x0.68 (coronal)
  space in
  > the T1-weighted CBV scan.
  >
  >
  > Any help would be appreciated
  >
  >
  > Usman

...

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