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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