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
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