Hi Freesurfers,
I would like to make sure I am using the funcroi commands correctly for anatomical and functional ROI analyses (using the aseg to anatomically constrain), and I have some questions about the commands.
If I want to extract the average percent signal change in the whole left amygdala for a particular contrast, is this the correct version of the commands to run?
1. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname> 2. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar 3. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt -c <contrast> -m cespct
If I want to extract the average percent signal change from an anatomically constrained functional ROI (e.g. an ROI representing activation in a certain contrast within the lh amygdala), is this the correct version of the commands to run:
4. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname> -contrast <contrast> -sign pos -thresh 1.3 5. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar 6. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt -a <analysisname> -c <contrast> -m cespct
My questions are (regarding the second set of commands):
-in the right hippocampus example under funcroi-config --help, the anatomical constraint is specified with --annot aseg.mgz 53, but it should be --seg aseg.mgz 53 like in my examples, correct? Otherwise you get an error. -Is it ok to use one analysis name in the funcroi-config file and another in funcroi-table-sess? Would that allow me to make an ROI from one analysis and use it to extract signal from another analysis? -If I get a message saying some subjects had "empty ROIs" and the value in the table for them is 0, does this mean that subjects had no activation (meeting the threshold specified) in the first contrast I specified (in funcroi-config) so no ROI could be created from their activation? -If I want to look at activation in more than one anatomical region (for example, bilateral amygdala), is there any way to do that with the -seg option?
Pardon the long message. Thanks for the help!
Emily