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 <mreu...@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 > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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