Alright thanks, mri_coreg looks a little better than bbregister. But similar to bbregister, using 6 dof results in a brain that is a little too small and using 12 dof has both scaling and translation issues.

What would be the way to use CVS? I tried using the m3z from mri_cvs_register as described in my first message, but got those weird artifacts (http://web.mit.edu/dsbeeler/www/images/m3z-mni.png).

DB

 ------------------------------------------------------------------------


Douglas N. Greve wrote:

Use mri_coreg instead of bbregister. Make sure to use 12 DOF. You could 
use CVS as well since that is non-linear

> ------------------------------------------------------------------------

On 05/07/2018 04:11 PM, David Beeler wrote:
>
>
> Hi Doug,
> Ok so if I am understanding correctly, SPM or FSL will be better at 
> registering functional data to CVS or MNI space for group analyses than 
> freesurfer will be because they have the capability of doing nonlinear 
> registrations. If that's the case I may give SPM a shot and compare the 
> results.
> But if I were to use freesurfer to do this registration, is there something 
> better than the following commands?:
> bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --bold
>
> mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
> --no-resample --nearest
> Adding --12 to bbregister and using the same mri_vol2vol as above actually 
> makes the transformation much worse, is there something I'm missing? I will 
> use SPM if I have to, but I feel like there is probably something smarter I 
> could be doing with freesurfer. And for clarification, is the --12 flag in 
> bbregister making the registration affine (ie accounting for translation, 
> rotation, scaling, and sheers)?
> Thanks again for your help, much appreciated!
> DB
> ------------------------------------------------------------------------
> Douglas N. Greve wrote:
> If that is really what you want to do, you should use a tool appropriate
> for this type of analysis (eg, SPM and FSL have non-linear intersubject
> registration)
> ------------------------------------------------------------------------
>
> On 05/04/2018 01:13 PM, David Beeler wrote:
> >
> >
> > Hi Doug,
> >
> > funcVol is an individual functional resting state scan. We are doing 
> > some clustering analyses and trying to visually compare the clustering 
> > across subjects (I would be a bit sketched out trying to quantify the 
> > overlap between subjects due to individual differences in anatomy, 
> > etc, but just looking at it might give us a clue on what is going on). 
> > We do all our analyses in the individual subject's native space, but 
> > it's hard to see what the similarities / differences are.
> >
> > If not bbregister, what would be the correct way to align all subjects 
> > to a common space?
> >
> > Thanks,
> > DB
> > ------------------------------------------------------------------------
> > Douglas N. Greve wrote:
> > What is funcVol? An individual functional? If so, then use --12 (12 dof
> > to account for scaling). In general, we don't recommend doing cross
> > subject registration with BBR as it is really not appropriate for that
> > kind of thing.
> > ------------------------------------------------------------------------
> > On 05/03/2018 01:30 PM, David Beeler wrote:
> >
> > Hi,
> >
> > I'm trying to register and transform some raw functional data 
> > (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low 
> > res dimensions.
> >
> > I have tried:
> > bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl 
> > --bold
> > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
> > --no-resample --nearest
> > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg 
> > --no-resample
> >
> > And this looks pretty good, but not perfect... the functional data is 
> > oriented correctly but the brain seems to be a centimeter or two 
> > smaller in multiple dimensions, see:
> >
> > http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png
> >
> > I'm not too surprised since the MNI brain is blurry and oddly round, 
> > but presumably there is a way to do this transformation more 
> > accurately. I've run mri_cvs_register for this subject using the --mni 
> > flag:
> >
> > mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir
> >
> > And for other applications I use this m3z file to transform volumes 
> > between MNI orig.mgz and individual subject orig.mgz, but is there a 
> > way to use it to transform functional data to MNI space while keeping 
> > the functional dimensions?
> >
> > I could do:
> >
> > mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz 
> > --reg register.dof6.lta --nearest --o template-in-anat.nii.gz
> >
> > mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz 
> > --mov template-in-anat.nii.gz --m3z 
> > $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o 
> > template-in-MNI-m3z.nii.gz --nearest
> >
> > But not only is this unideal because it requires upsampling the 
> > functional data to 256x256x256, it also gets these funky wavy distortions:
> >
> > http://web.mit.edu/dsbeeler/www/images/m3z-mni.png
> >
> >
> > Any thoughts are appreciated, thanks!
> >
> > -DB
> >
> >
> > _______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu
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