Hi Caroline, Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3.
Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.bee...@kuleuven.be> > wrote: > > Dear FS team, > > Apologies in advance for perhaps again a rather basic question. I attempted > to load the aparc overlay in freeview by using the written command from the > group analysis page, however it failed to load correctly. > > I used the following command: > freeview -f > fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 > -viewport 3d > è roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis > and dyslect is the contrast folder within this file (main effect of > dyslexia), containing a sig.mgh file (all seems fine) > > Unfortunately, I got an error that it does not recognize > “overlay_treshold=4,5”. I used freeview –h and tried certain commands alike, > but they didn’t work. When leaving out this part, I got another error that it > failed to recognize “annot_outline=1”. Again, leaving this out too, freeview > loads itself and the DK-regions become visible. However, nothing else seems > to get activated, and even not when putting “configure overlay” (which is set > to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. > When looking at the command line it says that it implemented the colortable > of DK-atlas (even twice), but it tells me nothing else. Also, after closing > and reloading Freeview by using the similar command and then clicking on > “configure overlay” the screen sometimes gets stuck, giving me the impression > that something must be wrong with the command. > > Could you please help me out and provide me the right command-line for > loading the overlay of the significance map of > “roi.lh.area.dyslect_basic.glmdir/dyslect”? > > Thanks in advance! > > Kind regards, Caroline > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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