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?

(2) how can I visualize contrasts created with -setwdelay?

 

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