Thanks a lot! That worked well! The registration is not perfect, but it is much
better than the original.
I used the command:
mri_vol2vol --mov PathTo/UnusualData.nii.gz --targ PathTo/orig.nii.gz --interp
nearest --o PathTo/UnusualData_toT1reg.nii.gz --reg PathTo/dti2t1.dat
Is there anything you would suggest that I run differently?
Aaron D. Jacobson
Technical Operations Manager
UCSD Center for Functional MRI
9500 Gilman Drive
La Jolla CA 92093-0677
On 4/20/17, 8:42 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
Yes, when using mri_vol2vol or mri_vol2surf, spec the unusual data set
as the --mov but pass the bbregister registration to the --reg flag.
On 04/20/2017 11:41 AM, Jacobson, Aaron wrote:
> Absolutely, thanks for looking into this.
>
> I have 3 datasets:
>
> 1. T1 anatomical
> 2. DTI
> 3. Unusual dataset (derived from DTI) that does not have a contrast that
bbregister can use to register the data
>
> I want to register the unusual dataset (#3) to the T1 anatomical.
>
> Since the unusual dataset cannot be read successfully by bbregister, I
registered the DTI to the anatomical and I would like to use the registration
parameters from that registration (DTI to t1) to register the unusual dataset
to the T1.
>
> Is this a possibility?
>
> Aaron D. Jacobson
> Technical Operations Manager
> UCSD Center for Functional MRI
> 9500 Gilman Drive
> La Jolla CA 92093-0677
>
>
>
> On 4/20/17, 8:09 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:
>
> I don't know what you are trying to do. Can you elaborate?
>
>
> On 04/19/2017 07:26 PM, Jacobson, Aaron wrote:
> > Hello,
> >
> > I am new to freesurfer. I have been looking for an answer to this
> > issue for days.
> >
> > I ran bbregister to align a dti scan to a t1 struc.
> >
> > It worked beautifully.
> >
> > I am trying to register a very abnormal looking dataset to the t1
> > using the registration parameters created during the first
bbregister
> > (dti to t1).
> >
> > I have been unable to figure this out, but it seems like it must
be a
> > common procedure. Any advice would be greatly appreciated.
> >
> >
> > _______________________________________________
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> > 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
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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--
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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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