answwers below On 09/27/2018 05:44 AM, 伊藤匠吾 wrote: > > > Hello, > > I am new to FreeSurfer. > > I conducted an experiment with event-related design. > There were eight non-fixation conditions. In every trial, a simple > stimulus was presented for about 1.5 sec, and the subject made a > button press. > > I did the following analyses: > > preproc-sess -df sessdirfile -s YY03 -per-run -fwhm 5 -sliceorder > siemens -surface fsaverage lhrh -mni305 -fsd bold > > mkanalysis-sess -a YY.sm5.lh -surface fsaverage lh -TR 2 -p OWN.par > -event-related -fsd bold -per-run -fwhm 5 -nconditions 8 -mcextreg > -fir 4 24 -polyfit 2 -force > > mkcontrast-sess -analysis YY.sm5.lh -contrast all_null -a 1 -a 2 -a 3 > -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -rmprestim > > selxavg3-sess -df sessdirfile -sf sessid -analysis YY.sm5.lh > > then, I checked the data with tksurfer-sess (tksurfer-sess -df > sessdirfile -s YY03 -analysis YY.sm5.lh -contrast all_null). > When clicked Overlay/Configure, I see Frame (0-8). Frame #1 shows > clear task-related activations (visual, auditory, motor areas). > Because I used -fir 4 24, I think I should have 12 time points, not 9. > I am currently using version 6, but I also checked the data with > version 5, confirmed the same outcome. > raw plots by tksurfer-sess (version 5) showed hemodynamic responses > for -4 sec to 20 sec. So the data seem to have correct length. > > Then, I created several contrasts with -setwdelay for all_null > weigting different time points like this > w1_all_null : 1 0 0 0 0 0 0 0 0 0 0 0 > w3_all_null : 0 0 1 0 0 0 0 0 0 0 0 0 > w5_all_null : 0 0 0 0 1 0 0 0 0 0 0 0 > w7_all_null : 0 0 0 0 0 0 1 0 0 0 0 0 > > with the following command, I see 4 frames, which probably correspond > to each contrast. > tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast > w1_all_null -contrast w3_all_null -contrast w5_all_null -contrast > w7_all_null > > However, when changing "frame" gives exactly the same image. > > (1) why did I get Frame (0-8) for my data that should have 12 frames? When you use -rmprestim, it subtracts the mean of the prestim baseline AND removes the prestim time points (-4 -2 and 0) so you only end up with 9 frames. > (2) how can I visualize contrasts created with -setwdelay? Your visualization command is correct. I don't understand why you are seeing the same image for each frame. Can you load them separately and see if they are different? > I would appreciate for any comments/suggestions. > > Here is my environment: > -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Users/guest/Documents/FreeSurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /usr/local/fsl > ------------------------------------------------------------------ > > Thank you! > Shoo > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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