Hi Eiran, there are a few modifications you need to make in your command lines to get to where you want to be.
1. funcroi-config -roi v1.rh.frame0 -label rh.V1 -analysis context_FIR.rh -frame 0 In this case, it does not make sense to specify a frame because the frame only applies to the sig map in a contrast, but you have not specified a contrast. I've just updated this cmd to prevent users from specifying a frame without specifying a contrast to prevent this confusion in the future. The way you have this set up is to create an ROI over all of V1 regardless of whether voxels are active or not (this is fine, just so you know what you are doing). 2. funcroi-table-sess -o v1.rh.frame0.table.txt -roi v1.rh.frame0 -a context_FIR.rh -s 0121_MC -map cespct Because you have not specified a contrast, it will get the mean of the meanfunc in the entire V1 label. In this case the -map argument is ignored (just changed to require a contrast with a -map). To have it get the cespct for the strongweak-vs-fix contrast, specify it with -c. Also, this will always get the mean of the first frame in cespct (remember the -frame in the config only is used to define the mask). If you want for it for a different frame, run funcroi-table-sess with the -frame option. So it looks like you only need to run funcroi-config once, then run funcroi-table-sess for each of your frames (assuming I know what it is you are trying to do). doug Eiran Vadim Harel wrote: > Hello, > > I did an FIR analysis and want to get the activation measure for specific ROI > at consequent time frames. > > mkanalysis-sess -analysis context_FIR.rh -surface fsaverage rh -fwhm 5 > -paradigm sca_wca.par -event-related -fir 4.4 17.6 -refeventdur 2.2 -mcextreg > -TR 2.2 -nconditions 2 -force > > mkcontrast-sess -analysis context_FIR.rh -contrast strongweak-vs-fix -a 1 > -a 2 -c 0 > > selxavg3-sess -s 0121_MC -analysis context_FIR.rh -force > > I then gave separate funcroi-config commands to each time frame 0-7 > > funcroi-config -roi v1.rh.frame0 -label rh.V1 -analysis context_FIR.rh > -frame 0 -force > > funcroi-table-sess -o v1.rh.frame0.table.txt -roi v1.rh.frame0 -a > context_FIR.rh -s 0121_MC -map cespct > > it created the text file with: > 0121_MC 84.034 > > when i ran it for the rest of the time frames it gave me the same number: > funcroi-config -roi v1.rh.frame7 -label rh.V1 -analysis context_FIR.rh > -frame 7 -force > > funcroi-table-sess -o v1.rh.frame7.table.txt -roi v1.rh.frame7 -a > context_FIR.rh -s 0121_MC -map cespct > It gave the same output in the text file: > 0121_MC 84.034 > > I am using freesurfer 5 on shimshon: > the project directory: /space/shimshon/2/users/eiran/contproc2 > SUBJECT_DIR- /space/shimshon/2/users/eiran/subjects > I made the frames according to your instructions on a request from dec. 2010 > with the same problem: > > > >> Currently, it is not as convenient to do this with version 5. You have >> to create a condition-vs-fixation for each condition that you want a >> time course for. Then for each condition, you need to run >> funcroi-table-sess for each time point (using the -frame option), then >> construct the waveforms from these files. It's a bit of a hassle, but >> scriptable. >> > > Thanks! > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
