Dear Ruopeng,
Yes, I'm running FS 5.3. :)
But then how can I see the correct significance overlay? Cause even when leaving out some commands (which may or may not work in 5.3), freeview does load, but seems to only display the DK-atlas on fs average (... and gets stuck sometimes too), as I described below.
I cant find the right command ...
So I guess my actual question is: Which command should i use to view a (correct) significance overlay in FS 5.3?
Thank you very much for your help!
Regards, Caroline
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.beelen@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 ? 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