Confuse playing around

code/1stlevel_design.fsf

@@ -106,7 +106,7 @@ set fmri(st_file) ""
 set fmri(bet_yn) 1
 
 # Spatial smoothing FWHM (mm)
-set fmri(smooth) 6
+set fmri(smooth) 4
 
 # Intensity normalization
 set fmri(norm_yn) 0
@@ -179,7 +179,7 @@ set fmri(thresh) 3
 set fmri(prob_thresh) 0.05
 
 # Z threshold
-set fmri(z_thresh) 2.3
+set fmri(z_thresh) 1.64
 
 # Z min/max for colour rendering
 # 0 : Use actual Z min/max
@@ -257,7 +257,7 @@ set fmri(regstandard_nonlinear_yn) 0
 set fmri(regstandard_nonlinear_warpres) 10 
 
 # High pass filter cutoff
-set fmri(paradigm_hp) 90
+set fmri(paradigm_hp) 100
 
 # Total voxels
 set fmri(totalVoxels) 38638080
@@ -270,10 +270,11 @@ set fmri(ncopeinputs) 0
 set feat_files(1) "/home/data/psyinf/forrest_gump/collection/visloc/src/aligned/###SUB###/in_bold3Tp2/###SUB###_task-objectcategories_###RUN###_bold"
 
 # Add confound EVs text file
-set fmri(confoundevs) 1
+set fmri(confoundevs) 0
 
 # Confound EVs text file for analysis 1
-set confoundev_files(1) "/home/data/psyinf/forrest_gump/collection/visloc/src/aligned/###SUB###/in_bold3Tp2/###SUB###_task-objectcategories_###RUN###_bold_mcparams.txt"
+#set confoundev_files(1) "/home/data/psyinf/forrest_gump/collection/visloc/src/aligned/###SUB###/in_bold3Tp2/###SUB###_task-objectcategories_###RUN###_bold_mcparams.txt"
+set confoundev_files(1) ""
 
 # EV 1 title
 set fmri(evtitle1) "bodies"
@@ -1056,7 +1057,7 @@ set fmri(con_orig1.5) 1
 set fmri(con_orig1.6) 1
 
 # Display images for contrast_orig 2
-set fmri(conpic_orig.2) 0
+set fmri(conpic_orig.2) 1
 
 # Title for contrast_orig 2
 set fmri(conname_orig.2) "FFA"
@@ -1080,7 +1081,7 @@ set fmri(con_orig2.5) -1.0
 set fmri(con_orig2.6) -1.0
 
 # Display images for contrast_orig 3
-set fmri(conpic_orig.3) 0
+set fmri(conpic_orig.3) 1
 
 # Title for contrast_orig 3
 set fmri(conname_orig.3) "PPA"
@@ -1104,7 +1105,7 @@ set fmri(con_orig3.5) 2.0
 set fmri(con_orig3.6) -1.0
 
 # Display images for contrast_orig 4
-set fmri(conpic_orig.4) 0
+set fmri(conpic_orig.4) 1
 
 # Title for contrast_orig 4
 set fmri(conname_orig.4) "EBA"
@@ -1128,7 +1129,7 @@ set fmri(con_orig4.5) -1.0
 set fmri(con_orig4.6) -1.0
 
 # Display images for contrast_orig 5
-set fmri(conpic_orig.5) 0
+set fmri(conpic_orig.5) 1
 
 # Title for contrast_orig 5
 set fmri(conname_orig.5) "LOC"
@@ -1152,7 +1153,7 @@ set fmri(con_orig5.5) 1.0
 set fmri(con_orig5.6) -5.0
 
 # Display images for contrast_orig 6
-set fmri(conpic_orig.6) 0
+set fmri(conpic_orig.6) 1
 
 # Title for contrast_orig 6
 set fmri(conname_orig.6) "VIS"

code/2ndlevel_design.fsf

@@ -30,7 +30,7 @@ set fmri(featwatcher_yn) 0
 set fmri(sscleanup_yn) 0
 
 # Output directory
-set fmri(outputdir) "/home/data/psyinf/forrest_gump/collection/visloc/###SUB###/2ndlvl_z164"
+set fmri(outputdir) "/home/data/psyinf/forrest_gump/collection/visloc/###SUB###/2ndlvl_z164_nomc"
 
 # TR(s)
 set fmri(tr) 3

code/compute_2ndlvl_glm.submit

@@ -11,33 +11,33 @@ transfer_executable = False
 initialdir = /home/data/psyinf/forrest_gump/collection/visloc
 executable = $ENV(FSLDIR)/bin/feat
 
-arguments = sub-01/2nd_z164.fsf
+arguments = sub-01/2nd_z164_nomc.fsf
 queue
-arguments = sub-02/2nd_z164.fsf
+arguments = sub-02/2nd_z164_nomc.fsf
 queue
-arguments = sub-03/2nd_z164.fsf
+arguments = sub-03/2nd_z164_nomc.fsf
 queue
-arguments = sub-04/2nd_z164.fsf
+arguments = sub-04/2nd_z164_nomc.fsf
 queue
-arguments = sub-05/2nd_z164.fsf
+arguments = sub-05/2nd_z164_nomc.fsf
 queue
-arguments = sub-06/2nd_z164.fsf
+arguments = sub-06/2nd_z164_nomc.fsf
 queue
-arguments = sub-09/2nd_z164.fsf
+arguments = sub-09/2nd_z164_nomc.fsf
 queue
-arguments = sub-10/2nd_z164.fsf
+arguments = sub-10/2nd_z164_nomc.fsf
 queue
-arguments = sub-14/2nd_z164.fsf
+arguments = sub-14/2nd_z164_nomc.fsf
 queue
-arguments = sub-15/2nd_z164.fsf
+arguments = sub-15/2nd_z164_nomc.fsf
 queue
-arguments = sub-16/2nd_z164.fsf
+arguments = sub-16/2nd_z164_nomc.fsf
 queue
-arguments = sub-17/2nd_z164.fsf
+arguments = sub-17/2nd_z164_nomc.fsf
 queue
-arguments = sub-18/2nd_z164.fsf
+arguments = sub-18/2nd_z164_nomc.fsf
 queue
-arguments = sub-19/2nd_z164.fsf
+arguments = sub-19/2nd_z164_nomc.fsf
 queue
-arguments = sub-20/2nd_z164.fsf
+arguments = sub-20/2nd_z164_nomc.fsf
 queue

code/generate_2nd_level_design.sh

@@ -19,7 +19,7 @@ executable = \$ENV(FSLDIR)/bin/feat
 
 EOT
 
-label="2nd_z164"
+label="2nd_z164_nomc"
 
 for sub in sub-*; do
   subid=$(echo "$sub" | cut -d '-' -f2-)

code/reg2std4feat

@@ -36,14 +36,14 @@ for featdir in $@; do
 	if [ "$inspace" != "$stdspace" ]; then
 		xfmdir="$tntsubdir/$inspace/in_$stdspace"
 		# check that we have the xfm info
-		[ $(imtest "$xfmdir/brain") -eq 1 ] && : || echo "cannot find transformation"
+		[ $(imtest "$xfmdir/head") -eq 1 ] && : || echo "cannot find transformation"
 		if [ -e "$xfmdir/xfm_12dof.mat" ]; then
 			tmpl2std_mat="$xfmdir/xfm_12dof.mat"
 		fi
 		if [ $(imtest "$xfmdir/subj2tmpl_warp") -eq 1 ]; then
 			tmpl2std_warp="$xfmdir/subj2tmpl_warp"
 		fi
-		imcp "$xfmdir/brain" "$regdir/standard"
+		imcp "$xfmdir/head" "$regdir/standard"
 	else
 		# we stay in the 
 		imcp "$tntsubdir/$inspace/brain" "$regdir/standard"