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.
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--
Sebastian Moeller
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