Doug, Thank you for the response. You are correct in that it was originally in native EPI space. I'll try out your suggestions.
Cheers On Fri, May 9, 2014 at 1:51 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > What space is the RS data in? If native functional space, I would > register to the anatomical (bbregister), then use mri_vol2vol with the > --fstal option > > On 05/08/2014 04:31 PM, Paul Beach wrote: > >> Hi Freesurfers, > >> > >> I have several processed resting time series files (processed through > >> AFNI) and I'd like to convert them to MNI space. I have done this > >> successfully for T1Volumes and some ROI masks using mri_convert and > >> tried to use the same code for the resting series. However, I've run > >> into a few issues - namely that the transformation cuts off part of > >> the top of the cortex. > >> > >> My code: > >> > >> /mri_convert -it nii -ot mgz CleanData_RestState.nii.gz > >> CleanData_RestState.mgz/ > >> / > >> / > >> /mri_convert CleanData_RestState.mgz --apply_transform > >> transforms/talairach.xfm \/ > >> /-oc 0 0 0 CleanData_RestState_talairach.mgz / > >> / > >> / > >> /mri_convert CleanData_RestState_talairach.mgz \ > >> cleanData_RestState_talairach.nii.gz/ > >> > >> > >> The final time series file, overlayed on the transformed T1Volume, is > >> below. > >> > >> Inline image 1 > >> > >> Any suggestions? > >> > >> > >> Thanks! > >> -- > >> Paul Beach > >> DO/PhD candidate - Year VI > >> Michigan State University > >> - College of Osteopathic Medicine > >> - Neuroscience Program > >> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) > > > > > > _______________________________________________ > > 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 > 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/ > > _______________________________________________ > 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. > > -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
_______________________________________________ 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.
