Just use mri_convert norm.mgz normInMNI.img --apply_transform transforms/talairach.xfm -oc 0 0 0 no need for the other arguments doug
On 12/15/2012 12:38 PM, Prasanna M wrote: > I had one more question: > What transform do I apply to get all the norm.mgz of all timepoints of > a subject to get the normalized image in MNI atlas space. Is this the > one inside mri/transforms/talairach.xfm? > More precisely, for all subjects, will something like this work? > mri_convert norm.mgz normInMNI.img --apply_transform > transforms/talairach.xfm -oc 0 0 0 -oni 256 -onj 256 -onk 256 -vs 1.0 > 1.0 1.0 --out_data_type float" > > Thanks, > Prasanna > > > On Thu, Dec 13, 2012 at 10:30 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Prasanna, the norm.mgz sounds like the best fit. Though I'm not > sure > what you mean by all the images registered to the 1st time point. > If you > are doing a longitudinal analysis, then following the longitudinal > stream will result in a set of norm.mgz's that will be in > alignment (but > not to the 1st time point, which you would not want because it > causes bias). > doug > > > On 12/13/2012 12:28 PM, Prasanna M wrote: > > I ran Freesurfer on OASIS longitudinal data with the longitudinal > > pipeline. I want to work with the full brain image (with gray level > > intensities) which is intensity normalized and skull stripped > and all > > the timepoints of a subject are rigidly registered to the 1st time > > point. There were many brain mgz files created during the > processing. > > What is the best final image which I should be working with? > > > > Thanks, > > Prasanna > > > > -- > > -- > > Let there be peace on earth... > > And let it begin with me. > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > -- > -- > Let there be peace on earth... > And let it begin with me. > > -- 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: 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
