Yea, you need to do it in the two steps you mention. You can do that
from one command line with something like
bbregister --s subject --mov epi.nii --init-{fsl,header} --bold --int
aascout.nii --o register.dat
The --int is an "intermediate" volume.
doug
Andrew Dumas wrote:
> That did the trick, thank you! As for using bbregister, I haven't had
> any luck using bbregister for the partial volume EPIs... they're always
> off. We have a strange protocol where only the functionals get the
> 32-channel coil, so right before the EPIs get done I have an AAscout
> image. I've been using bbregister to align the FS MPRAGE scans with the
> AAscout (first frame), then using that registration on the EPIs. It
> seems to come out a LOT better than using bbregister on EPIs directly.
>
> Andrew
>
>
> On Tue, 2011-12-20 at 14:58 -0500, Douglas N Greve wrote:
>
>> Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or
>> --talres 1 for 1mm isotropic) option. This will put it into an MNI305
>> space. So something like
>>
>> mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o
>> yourvolume.mni305.nii
>>
>> If you did not create the register.dat with bbregister, I would strongly
>> suggest it. It works really well on the partial volume files. If you do,
>> you should specify your current register.dat as the init registration.
>>
>> doug
>>
>> Andrew Dumas wrote:
>>
>>> Hi,
>>>
>>> I'm trying to move a bunch of partial FOV functional images (occipital
>>> cortex only with oblique coronal slices) into common space. For each
>>> subject, I have a registration file (register.dat) to register
>>> functional images to anatomicals, and I'd like to incorporate the
>>> talairach.xfm registration so that I have a matrix that registers the
>>> functional images to the mni305 volume. I've been using the following,
>>> but registrations aren't coming out properly:
>>>
>>> mri_matrix_multiply -im register.dat -iim
>>> <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat
>>>
>>> I'm checking them using tkregister2, but the results don't look great.
>>> Is there a better/easier way to do this? Thanks!
>>>
>>> Andrew
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>>
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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