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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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.