On 12/12/2013 10:08 AM, Emily Boeke wrote: > 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. Oops, you're right. I've made the change in our tree. > -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? Yes > -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? Correct > -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? The way to do this is to create a new segmentation for each subject that contains only the amyg, eg, mri_binarize --i aseg.mgz --match 18 54 --o amyg.mgz This creates a mask of the amygdalae in which the amygdala voxels = 1 and everything else is 0 Then specify --seg amyg.mgz 1 Use 1 here because the amygdala voxels = 1
doug > > Pardon the long message. Thanks for the help! > > Emily > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
