Yes, it does MC then STC. This is a chronic problem that has never been solved. If you do STC first and there is significant motion, then the STC will be wrong. They really need to be done simultaneously. However, if you use an ascending or descending slice acq (instead of interleaved), then this issue mostly goes away and you can safely do MC before STC. doug
On 02/01/2013 03:13 PM, Katie Bettencourt wrote: > Can you tell me the order of the slice timing and motion correction > steps in preproc-sess (freesurfer v 4.5)? From the wiki it looks like > motion correction is done first (For MC the input will be f and the > output will be fmc For STC the input will be fmc and the output will > be fmcstc". However, wouldn't doing the motion correction first cause > an issue? Because, otherwise, after motion correction, the slices are > realigned and the timing of a slice at a particular location is no > longer what it is before, correct? > > Can you clarify this for me? > > > _______________________________________________ > 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: 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.
