Hi all,<br><br>I&#39;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&#39;ve previously found), and I&#39;m not sure what&#39;s going on.<br>

<br>I&#39;m running Freesurfer 4.5 on red hat linux.<br><br>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&lt;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.<br>

<br>% signal change:<br>110222SKJ_connected     110222SP_connected <br>0.000988998467052       0.000533852720367 <br>0.00105349836708        0.000556814127695 <br>0.000408499366826       0.000327200054419 <br>0.000440749316839       0.000436266739225 <br>

<br>commands:<br>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<br>

<br>mkcontrast-sess -analysis connect -contrast connected_vs_unconnected -a 1 -c 2<br>mkcontrast-sess -analysis connect -contrast connected_vs_noise -a 1 -c 3<br>mkcontrast-sess -analysis connect -contrast connected_vs_phase -a 1 -c 4<br>

mkcontrast-sess -analysis connect -contrast connected_vs_fix -a 1 -c 0<br>mkcontrast-sess -analysis connect -contrast unconnected_vs_noise -a 2 -c 3<br>mkcontrast-sess -analysis connect -contrast unconnected_vs_phase -a 2 -c 4<br>

mkcontrast-sess -analysis connect -contrast unconnected_vs_fix -a 2 -c 0<br>mkcontrast-sess -analysis connect -contrast noise_vs_phase -a 3 -c 4<br>mkcontrast-sess -analysis connect -contrast noise_vs_fix -a 3 -c 0<br>mkcontrast-sess -analysis connect -contrast shape_vs_noise -a 1 -a 2 -c 3<br>

mkcontrast-sess -analysis connect -contrast shape_vs_phase -a 2 -a 1 -c 4<br>mkcontrast-sess -analysis connect -contrast shape_vs_noisephase -a 2 -a 1 -c 3 -c 4<br>mkcontrast-sess -analysis connect -contrast act_vs_fix -a 2 -a 1 -a 3 -a 4 -c 0<br>

<br>selxavg3-sess -sf connect-sess -df connect.dir -analysis connect<br><br>#run ROIs<br>setenv anal connect<br>foreach roi ( infIPS supIPS loc )<br>foreach h (lh rh)<br>func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal -anatlabel ips_loc/${roi}-${h} -sf connect-sess  -df connect.dir<br>

roisummary-sess  -sumfile ips-rois/${anal}_${roi}-${h}.dat -roidef ${roi}-${anal}-${h} -analysis ${anal} -sf connect-sess  -df connect.dir<br>python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f ips-rois -c 4<br>end<br>end<br>

<br>Thanks,<br><br>Katie<br><br>