Hi Martin,
Thanks for the suggestion. I resolved the issue by using the --regheader flag in tkmregister, and --reg as the default output by mri_vol2vol (even though I did supply a reg-final flag). It seems like I mixed up the difference between reg-final and the default registration matrix. would you mind explaining the difference? in any event, here is my script:

for i in $(ls posterior_left_* posterior_Left-Hippocampus.mgz posterior_right_* posterior_Right-Hippocampus.mgz); do

fname=$(basename $i); fname=${fname%%.*};

echo "$fname"

tkregister2 --noedit --reg hc_subfields/xfm_"$fname".mgz.reg --regheader --targ nu.mgz --mov "$i" --ltaout hc_subfields/xfm_"$fname".lta

mri_concatenate_lta hc_subfields/xfm_"$fname".lta xfm_nu_to_pre.lta hc_subfields/xfm_"$fname"_to_pregado.lta

mri_convert -at hc_subfields/xfm_"$fname"_to_pregado.lta "$i" hc_subfields/final/final_"$fname".mgz;

done

Thanks,

Usman

On Jul 10, 2012, at 10:40 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:

Hi Usman ,

Try validating each step by applying each transform. I usually use mri_convert -at
For it.

Best Martin

Usman Khan <usman@bwh.harvard.edu> 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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