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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
