Ok, I ran that and a couple questions. I ran it on 2 different subjects and got the exact same value, is that expected? Do I need to run it for each subject?
Also, do I need to do this for event-related designs as well, or just block designs? I tried to run it on another analysis I did, an event-related one, but got this error:
??? Error using ==> times Matrix dimensions must agree.
Katie
On Mon, Apr 11, 2011 at 12:22 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You can run it anytime after the analysis. The 'X' file below is an actual file that is there (X.mat). The value that you get out of this procedure should be used to multiply the values you get out of roisummary-sess.
doug
Katie Bettencourt wrote:
I'm working with Yaoda Xu. Thanks for the percent signalchange fix, but I"m a little confused by what you wrote. When do I run that? after running roisummary-sess? Or after the analysis is run?
Also, is the load('X' a placeholder where I need to put load('filename')? or will it just work as is? Obviously I change the session and analysis in the cd line. And isthat a flat scale factor for all conditions for that subject?
Katie On Fri, Apr 8, 2011 at 10:59 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: btw, I notice that you have a harvard email now (was BU). who are you working with there? doug Katie Bettencourt wrote: Hi all, I'm doing ROI analysis on functional data with an anatomical label, and while the activity looks strong and robust in tksurfer, the % signal changes I am getting are very low (and much lower than we've previously found), and I'm not sure what's going on. I'm running Freesurfer 4.5 on red hat linux. The design is a blocked design with 4 non-null conditions, baseline is fixation. Attached is a picture of the activity I get for 2 subjects for on of the conditions vs fixation (baseline) at a p<0.05 threshold with the ROI outlined in black as well as the output from roisummary-sess for these two subjects in that roi. I calculate % signal change based of the output from roisummary-sess, dividing each condition by the baseline in that file and then multiplying by 100. % signal changes are listed below, along with all commands run. % signal change: 110222SKJ_connected 110222SP_connected 0.000988998467052 0.000533852720367 0.00105349836708 0.000556814127695 0.000408499366826 0.000327200054419 0.000440749316839 0.000436266739225 commands: mkanalysis-sess -analysis connect -TR 2 -paradigm connect.dat -designtype blocked -funcstem fmc -motioncor -runlistfile connect_runs.txt -inorm -tpexclude tpexclude.dat -nconditions 4 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis connect -contrast connected_vs_unconnected -a 1 -c 2 mkcontrast-sess -analysis connect -contrast connected_vs_noise -a 1 -c 3 mkcontrast-sess -analysis connect -contrast connected_vs_phase -a 1 -c 4 mkcontrast-sess -analysis connect -contrast connected_vs_fix -a 1 -c 0 mkcontrast-sess -analysis connect -contrast unconnected_vs_noise -a 2 -c 3 mkcontrast-sess -analysis connect -contrast unconnected_vs_phase -a 2 -c 4 mkcontrast-sess -analysis connect -contrast unconnected_vs_fix -a 2 -c 0 mkcontrast-sess -analysis connect -contrast noise_vs_phase -a 3 -c 4 mkcontrast-sess -analysis connect -contrast noise_vs_fix -a 3 -c 0 mkcontrast-sess -analysis connect -contrast shape_vs_noise -a 1 -a 2 -c 3 mkcontrast-sess -analysis connect -contrast shape_vs_phase -a 2 -a 1 -c 4 mkcontrast-sess -analysis connect -contrast shape_vs_noisephase -a 2 -a 1 -c 3 -c 4 mkcontrast-sess -analysis connect -contrast act_vs_fix -a 2 -a 1 -a 3 -a 4 -c 0 selxavg3-sess -sf connect-sess -df connect.dir -analysis connect #run ROIs setenv anal connect foreach roi ( infIPS supIPS loc ) foreach h (lh rh) func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal -anatlabel ips_loc/${roi}-${h} -sf connect-sess -df connect.dir roisummary-sess -sumfile ips-rois/${anal}_${roi}-${h}.dat -roidef ${roi}-${anal}-${h} -analysis ${anal} -sf connect-sess -df connect.dir python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f ips-rois -c 4 end end Thanks, Katie
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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