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.eduwrote:
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
- 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
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