Luis and Sebastian, you are right that -toff is not accepted anymore. The way that the motion correction (and func-anat reg) work now is that a functional template is created, and this template is used as the reference for MC and reg. This prevents the user from using a different template for each. The template is created with mktemplate-sess. By default, this will use the middle time point, but you can spec any time point that you want with the -frame option. Run with -help to get more info.
doug Sebastian Moeller wrote: > Hi Luis, > > On Nov 28, 2010, at 16:48 , Luis Lafer-Sousa wrote: > > >> We are having an issue with scripts we used in freesurfer 4.5.0 but no >> longer work in 5.0.0. It is the mc-sess step, and we receive: >> >> ERROR: Flag -toff unrecognized. >> -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0 >> > > judging from ./tmp_run_list you might be using scripts similar to the > ones I use... (then again I might be wrong), but my scripts will definitely > cause the same problems for me,,, > > >> Done... >> >> On the wiki, that flag is still recognized. When we delete it, we >> then receive a "by run" or "by session" error. I suspect this has >> something to do with the freesurfer or AFNI update, but we do not know >> what the new mc-sess takes as tags since the wiki has not changed. >> Does anybody know how mc-sess has changed? >> > > Have a look at $FREESURFER_HOME/fsfast/bin/mc-sess thgis is the script > that gets called. It looks like the target offset is not "wired" inside this > script anymore. I seem to recall that Doug recommends to moco each run to its > middle frame now. I do think it would be great if we still had the option to > specify one frame from a single run as target for motion correction for > non-human primates. The reason being the following: > Occasionally (more often than one would like) some frames in monkey scans are > really distorted due to the monkey displacing the field lines during a TR; in > the past it was an improvement for the moco to pick a frame that was not > affected by these artifacts. (Even using EPI unwarping with a fieldmap and > fancy phased array coils does not remove this problem fully). This is going > to be tricky if mc-sess insist on the middle frame for each run (as some of > those might be really rotten). > Doug, do you think it would be possible to resurrect the possibility to > specify toff and run (I think a number of monkey researchers would be happy). > > Best > Sebastian > > > >> Thank you, >> Luis L.S. >> _______________________________________________ >> 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. >> >> > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
