OK Thanks. But a couple of clarification questions:
1) I take it that running mri_fill and then running inflate_subject-?h is equivalent to running inflate_subject? 2) The "tesselation" component of Create Surface does not need to be rerun separately? 3) wanted to mention that p. 53 of the Tutorial describes using inflate_subject-?h without mentioning mri_fill. Thanks, Al On Fri, 14 Dec 2001, Bruce Fischl wrote: > Hi Al, > > after editing you *must* rerun mri_fill, otherwise no editing changes will > be used (since it regenerates the filled volume from the wm, and it is the > wm that you edit). Note that inflate_subject-lh and -rh *don't* rerun > mri_fill, that is done in inflate_subject before calling the -lh and -rh. > As far as the 0.0 minutes problem, you'll have to send along a log file (if > it still occurs). > > cheers, > Bruce > > > > On Fri, 14 Dec 2001, Albert Kim wrote: > > > > > Dear all, > > I hope someone will have insight into the following problem: > > > > I've had trouble with the use of "inflate_subject-rh" & > > "inflate_subject-lh", after manually editing the large defects in the > > reconstruction (e.g., p. 53 of the Tutorial). Confusingly, this took > > two forms. On one occasion, after editing the right hemisphere's > > defects, I ran: > > inflate_subject-rh E12410 > > > > This completed in "0.0 minutes" and created empty output files. > > That is, the files rh.orig, rh.inflated, etc, which had previously > > contained surface information, are now empty. > > > > On a second occasion, after editing the LEFT hemisphere, I ran: > > inflate_subject-lh E12410 > > > > This time, the various surface files were not erased, but were instead > > left unchanged---the manual editing of defects was not incorporated. > > > > In both cases, I am able to recreate surfaces by running CREATE > > SURFACE in the GUI. During the CREATE SURFACE process, Freesurfer > > prompts me about overwriting various files. I'm guessing perhaps that > > the over-writing of the various surface files is part of the problem > > here. Has anybody got confirmation of this problem or solutions? > > > > Al Kim > > Dept of Psychology > > University of Washington > > > > > > > >
