View source for Lab05

=Downloads=
[[media:Lab05data.tar.gz|Dataset and scripts]] (type "tar xvf Lab05data.tar.gz" to extract)

=Linux=

#create symbolic link to a path
<pre>
ln -s <destination> <symbolic link>
</pre>

: For example, typing the following command in your home directory (~):
<pre>
ln -s /media/DATA2/guests/public/Lab05 fmric
</pre>

: Create a symbolic link "fmric" pointing to "/media/DATA2/guests/public/Lab05" (assuming it exists). Thus, under your home directory, type:
<pre>
cd fmric
</pre>

you will be in "~/fmric", where all the contents of /media/DATA2/guests/public/Lab05 can be accessed. 
*Note: Deleting the symbolic link won't remove the contents of its destination.

#Loop with tcsh
<pre>
foreach <variable> (<list items>)

<your command>

end
</pre>

The statements above will iterate <your command> for the length of your list items. 

<pre>
Example:

#!/usr/bin/tcsh

foreach run (1 2 3)

   echo $run

end

</pre>
=Single Subject General Linear Model (GLM)=
*Analysis of 1 run (ana01)
<pre>
3dDeconvolve -input pb03.FT_epi_r1.scale+orig.HEAD         	         \
	-polort 3                                                        \
	-num_stimts 2                                                    \
	-stim_times 1 stimuli/AV1_vis_1run.txt 'BLOCK(20,1)'             \
	-stim_label 1 Vrel                                               \
	-stim_times 2 stimuli/AV2_aud_1run.txt 'BLOCK(20,1)'             \
	-stim_label 2 Arel                                               \
	-gltsym 'SYM: Vrel -Arel'                                        \
	-glt_label 1 V-A                                                 \
	-fout -tout -x1D X.xmat.1D -xjpeg X.jpg                          \
	-fitts fitts.FT                                       		 \
	-errts errts.FT                                             	 \
	-bucket stats.FT
</pre>

*Analysis of 1 run with motion parameters (ana02)
<pre>
3dDeconvolve -input pb03.FT_epi_r1.scale+orig.HEAD          	         \
	-polort 3                                                        \
	-num_stimts 8                                                    \
	-stim_times 1 stimuli/AV1_vis_1run.txt 'BLOCK(20,1)'             \
	-stim_label 1 Vrel                                               \
	-stim_times 2 stimuli/AV2_aud_1run.txt 'BLOCK(20,1)'             \
	-stim_label 2 Arel                                               \
	-stim_file 3 dfile.rall.1D'[0]' -stim_base 3 -stim_label 3 roll  \
	-stim_file 4 dfile.rall.1D'[1]' -stim_base 4 -stim_label 4 pitch \
	-stim_file 5 dfile.rall.1D'[2]' -stim_base 5 -stim_label 5 yaw   \
	-stim_file 6 dfile.rall.1D'[3]' -stim_base 6 -stim_label 6 dS    \
	-stim_file 7 dfile.rall.1D'[4]' -stim_base 7 -stim_label 7 dL    \
	-stim_file 8 dfile.rall.1D'[5]' -stim_base 8 -stim_label 8 dP    \
	-gltsym 'SYM: Vrel -Arel'                                        \
	-glt_label 1 V-A                                                 \
	-fout -tout -x1D X.xmat.1D -xjpeg X.jpg                          \
	-fitts fitts.FT                                               	 \
	-errts errts.FT                                               	 \
	-bucket stats.FT

</pre>
*analysis of 3 runs with motion parameters
<pre>
3dDeconvolve -input pb03.FT_epi_r?.scale+orig.HEAD          	         \
	-polort 3                                                        \
	-num_stimts 8                                                    \
	-stim_times 1 stimuli/AV1_vis.txt 'BLOCK(20,1)'                  \
	-stim_label 1 Vrel                                               \
	-stim_times 2 stimuli/AV2_aud.txt 'BLOCK(20,1)'                  \
	-stim_label 2 Arel                                               \
	-stim_file 3 dfile.rall.1D'[0]' -stim_base 3 -stim_label 3 roll  \
	-stim_file 4 dfile.rall.1D'[1]' -stim_base 4 -stim_label 4 pitch \
	-stim_file 5 dfile.rall.1D'[2]' -stim_base 5 -stim_label 5 yaw   \
	-stim_file 6 dfile.rall.1D'[3]' -stim_base 6 -stim_label 6 dS    \
	-stim_file 7 dfile.rall.1D'[4]' -stim_base 7 -stim_label 7 dL    \
	-stim_file 8 dfile.rall.1D'[5]' -stim_base 8 -stim_label 8 dP    \
	-gltsym 'SYM: Vrel -Arel'                                        \
	-glt_label 1 V-A                                                 \
	-fout -tout -x1D X.xmat.1D -xjpeg X.jpg                          \
	-fitts fitts.FT                                               	 \
	-errts errts.FT                                               	 \
	-bucket stats.FT
</pre>

=References=
[http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht03_stim/html/AFNI_howto.html stimulus timing tutorial ]