From 806e6f8d6bb25c1024e6b2ae411952733508f754 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Tue, 11 Oct 2011 17:18:21 -0400
Subject: [PATCH 01/30] Wrote scaffold of new code

---
 svmbatch/README      |  0
 svmbatch/filelist1   |  0
 svmbatch/filelist2   |  0
 svmbatch/svmbatch.sh | 36 ++++++++++++++++++++++++++++++++++++
 svmbatch/svmdir      |  0
 5 files changed, 36 insertions(+)
 create mode 100644 svmbatch/README
 create mode 100644 svmbatch/filelist1
 create mode 100644 svmbatch/filelist2
 create mode 100644 svmbatch/svmbatch.sh
 create mode 100644 svmbatch/svmdir

diff --git a/svmbatch/README b/svmbatch/README
new file mode 100644
index 00000000..e69de29b
diff --git a/svmbatch/filelist1 b/svmbatch/filelist1
new file mode 100644
index 00000000..e69de29b
diff --git a/svmbatch/filelist2 b/svmbatch/filelist2
new file mode 100644
index 00000000..e69de29b
diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
new file mode 100644
index 00000000..e0c3fd4b
--- /dev/null
+++ b/svmbatch/svmbatch.sh
@@ -0,0 +1,36 @@
+#!/bin/sh
+
+#List of some useful variables
+
+
+filelist1=`cat filelist1`
+filelist2=`cat filelist2`
+svmdir=`cat svmdir`
+
+
+
+3dbucket -sessiondir $svmdir -prefixname bucket1 $filelist1
+3dbucket -sessiondir $svmdir -prefixname bucket2 $filelist2
+
+cd $svmdir
+
+3dbucket -prefixname bucket bucket1 bucket2
+
+3dcalc -a bucket -expr "a" -prefixname shortbucket -datum short
+
+3dTcat -prefix timeshortbucket shortbucket
+
+for i in $filelist1
+do
+echo 1 >>labels.1D
+done
+
+for i in $filelist2
+do
+echo 2 >> labels.1D
+done
+
+3dAutomask timeshortbucket
+
+3dsvm -trainvol timeshortbucket -trainlabels labels.1D -mask automask -model model -bucket bucket
+
diff --git a/svmbatch/svmdir b/svmbatch/svmdir
new file mode 100644
index 00000000..e69de29b

From dfae375fd58ce18bf671a28ec8b4596cc42bb540 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Thu, 13 Oct 2011 14:31:45 -0400
Subject: [PATCH 02/30] First skeleton of svmbatch.sh written

Fixed file references to include '+orig'. Successful test run through on garbage data

Updated readme file
---
 svmbatch/README      | 27 +++++++++++++++++++++++++++
 svmbatch/svmbatch.sh | 33 ++++++++++++++++++++++-----------
 2 files changed, 49 insertions(+), 11 deletions(-)

diff --git a/svmbatch/README b/svmbatch/README
index e69de29b..5d57114d 100644
--- a/svmbatch/README
+++ b/svmbatch/README
@@ -0,0 +1,27 @@
+SVM Batch
+
+Written 2011 by Daniel Kessler, kesslerd@umich.edu
+
+**Prerequisites**
+This was code was written and tested in AFNI_2011_05_26_1457
+
+
+This batch script should not require any modification by you. Instead, you customize it by editing the support text files that come with it, namely:
+
+*svmdir
+This file should contain a path to an extant directory where the script should store all of its intermediates and results
+
+*filelist1
+This should contain a whitespace-delimted list of (ideally absolute) paths to files that 3dsvm will consider to be examples of class 1. If you are giving it data from img/hdr pairs, be sure to point to the hdr (it will figure out where the img is based on the hdr).
+
+*filelist2
+Just like filelist1, except these are files that represent examples from class 2.
+
+That's it. Other support files may be added as we extend functionality.
+
+
+**Likely future additions
+
+1) Automatic testing of model on training set
+2) Automated partitioning of examples into training set and test set for model cross-validation
+3) Permutation testing. This will be computationally intensive, but not too hard to implement.
diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index e0c3fd4b..3908964e 100644
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -1,24 +1,28 @@
-#!/bin/sh
-
-#List of some useful variables
-
+#!/bin/bash
 
+ 
+#Read in variable values from associated files
 filelist1=`cat filelist1`
 filelist2=`cat filelist2`
 svmdir=`cat svmdir`
 
-
-
+#Build bucket files out of each of your conditions
 3dbucket -sessiondir $svmdir -prefixname bucket1 $filelist1
 3dbucket -sessiondir $svmdir -prefixname bucket2 $filelist2
 
+#Change to the svm working directory (presumably where this script was called from)
 cd $svmdir
 
-3dbucket -prefixname bucket bucket1 bucket2
+#Combine your two class bucket files into one super bucket
+3dbucket -prefixname bucket bucket1+orig bucket2+orig
+
+#Convert your bucket file to shorts
+3dcalc -a bucket+orig -expr "a" -prefixname shortbucket -datum short
 
-3dcalc -a bucket -expr "a" -prefixname shortbucket -datum short
+#Convert your short bucket to be of type "time" (required by 3dsvm)
+3dTcat -prefix timeshortbucket shortbucket+orig
 
-3dTcat -prefix timeshortbucket shortbucket
+#Build filelist by appending 1s or 2s to label file based on number in each class category
 
 for i in $filelist1
 do
@@ -30,7 +34,14 @@ do
 echo 2 >> labels.1D
 done
 
-3dAutomask timeshortbucket
+#Build a mask (in the future we may want to learn more about these options, or allow for specification of a custom mask
+3dAutomask timeshortbucket+orig
+
+#Run your 3dsvm model
+3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D -mask automask+orig -model model -bucket weightbucket
 
-3dsvm -trainvol timeshortbucket -trainlabels labels.1D -mask automask -model model -bucket bucket
 
+##To add:
+#1) Model testing (on training data itself, be sure to use set detrend to no
+#2) Ability to automatically split examples into training and test set, and do cross validation randomly
+#3) Permutation tests (basically just a for loop with random permutation of labels file. Tricky thing is querying test model weights against giant population of permutation weights
\ No newline at end of file

From 8038ad4498f4a345d5caa5386378ecc75ed2dd3e Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 24 Oct 2011 16:07:46 -0400
Subject: [PATCH 03/30] Added two functions to the shell script.

1] If directory specified by svmdir doesn't exist, it will attempt to make it for you.

2] If you give the script an additional argument of 1, it will run a leave-one-out crossvalidation for you.
---
 svmbatch/svmbatch.sh | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 3908964e..530a140d 100644
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -6,6 +6,11 @@ filelist1=`cat filelist1`
 filelist2=`cat filelist2`
 svmdir=`cat svmdir`
 
+if [ ! -d $svmdir ]
+then
+    mkdir $svmdir
+fi
+
 #Build bucket files out of each of your conditions
 3dbucket -sessiondir $svmdir -prefixname bucket1 $filelist1
 3dbucket -sessiondir $svmdir -prefixname bucket2 $filelist2
@@ -38,8 +43,14 @@ done
 3dAutomask timeshortbucket+orig
 
 #Run your 3dsvm model
-3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D -mask automask+orig -model model -bucket weightbucket
+if [ $1 == 1 ]
+then
+    3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D -mask automask+orig -model model -bucket weightbucket -x 1
+
+else
+    3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D -mask automask+orig -model model -bucket weightbucket
 
+fi
 
 ##To add:
 #1) Model testing (on training data itself, be sure to use set detrend to no

From 917b94c958813b3aa5930a16171002c34045c143 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Fri, 2 Dec 2011 12:56:57 -0500
Subject: [PATCH 04/30] Huge update to svmbatch.

Added ability to do totem mode, significant rearrangement of argument/parameter processing, etc.
---
 svmbatch/svmbatch.sh | 88 +++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 82 insertions(+), 6 deletions(-)
 mode change 100644 => 100755 svmbatch/svmbatch.sh

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
old mode 100644
new mode 100755
index 530a140d..14fa43f6
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -1,7 +1,58 @@
 #!/bin/bash
 
- 
+#A program to perform SVM based only on lists of files
+
+#CONSTANTS
+
+#FUNCTIONS
+
+function totembatch {
+    #Given a filelist, suffixlist, and totem directory, loop over
+    #combinations of filelist and suffixlist, and build totems
+
+    totemsuf=`cat totem.suf`
+    
+    for  file in $1; do
+	totemlist=  #Clear the totemlist variable. This will hold the list of all the subfiles going into your totem
+	for suf in $totemsuf; do
+		totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
+	done
+	newname=`echo $file | sed 's:/:_:2g'` #edit the filename to have underscores instead of slashes, it will keep the temp directory cleaner
+	fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
+	newname=
+    done
+}
+
+
+#Parameter Processing
+
+totem=
+crossv=
+totemtemp=/tmp/totems #Where to store your totem files/examples
+
+
+while [ "$1" != "" ]; do
+    case $1 in
+	-t | --totem )	totem=1  #Operate in totem stacking mode
+			shift
+			#totemtemp=$1
+			echo Running in Totem Mode
+			;;
+	-c | --crossv )	crossv=1 #Will perform cross validation
+			
+    esac
+    shift
+done
+       
+
+##Main Function
+
+
+
 #Read in variable values from associated files
+
+
+
 filelist1=`cat filelist1`
 filelist2=`cat filelist2`
 svmdir=`cat svmdir`
@@ -11,6 +62,20 @@ then
     mkdir $svmdir
 fi
 
+#if in totem mode
+
+if [ "$totem" == 1 ]; 
+    then
+    mkdir $totemtemp
+    totembatch "$filelist1"
+    totembatch "$filelist2"
+
+    filelist1=`cat filelist1 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'` #Update the filelist to point to where the totem-ed files are
+    filelist2=`cat filelist2 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'`
+
+
+fi
+
 #Build bucket files out of each of your conditions
 3dbucket -sessiondir $svmdir -prefixname bucket1 $filelist1
 3dbucket -sessiondir $svmdir -prefixname bucket2 $filelist2
@@ -42,16 +107,27 @@ done
 #Build a mask (in the future we may want to learn more about these options, or allow for specification of a custom mask
 3dAutomask timeshortbucket+orig
 
-#Run your 3dsvm model
-if [ $1 == 1 ]
+#maskrule="-mask automask+orig"
+if [ "$totem" = "1" ]
 then
-    3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D -mask automask+orig -model model -bucket weightbucket -x 1
+    maskrule="-nomodelmask"
+fi
 
-else
-    3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D -mask automask+orig -model model -bucket weightbucket
+crossvrule=""
+if [ "$crossv" = "1" ]
+then
+    crossvrule="-x 1"
+fi
 
+#Run your 3dsvm model
+3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D $maskrule -model model -bucket weightbucket $crossvrule
+
+if [ "$totem" = "1" ] #delete your temporary totem files, if they existed
+then
+    rm $totemtemp -rf
 fi
 
+
 ##To add:
 #1) Model testing (on training data itself, be sure to use set detrend to no
 #2) Ability to automatically split examples into training and test set, and do cross validation randomly

From 074a764528238ed621ad6a0a3c1ab7442a0ecf1b Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 5 Dec 2011 17:09:16 -0500
Subject: [PATCH 05/30] Added kernel and directory support to SVM batch options

---
 svmbatch/svmbatch.sh | 30 ++++++++++++++++++++++++------
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 14fa43f6..c919752b 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -34,11 +34,17 @@ totemtemp=/tmp/totems #Where to store your totem files/examples
 while [ "$1" != "" ]; do
     case $1 in
 	-t | --totem )	totem=1  #Operate in totem stacking mode
-			shift
+			#shift
 			#totemtemp=$1
 			echo Running in Totem Mode
 			;;
-	-c | --crossv )	crossv=1 #Will perform cross validation
+	-c | --crossv )	crossv=1;; #Will perform cross validation
+	-k | --kernel ) kernelmode=1 #Kernel has been specified
+			shift
+			kernel=$1
+			echo Kernel specified is $kernel
+			;;
+	-d | --directory ) shift ; svmdir=$1
 			
     esac
     shift
@@ -55,7 +61,11 @@ done
 
 filelist1=`cat filelist1`
 filelist2=`cat filelist2`
-svmdir=`cat svmdir`
+
+if [ -f svmdir ]
+then
+    svmdir=`cat svmdir`
+fi
 
 if [ ! -d $svmdir ]
 then
@@ -113,14 +123,21 @@ then
     maskrule="-nomodelmask"
 fi
 
-crossvrule=""
+crossvrule="-x 1"
 if [ "$crossv" = "1" ]
 then
     crossvrule="-x 1"
 fi
 
+if [ "$kernelmode" = "1" ] #if running in kernel mode
+then
+	kernelrule="-kernel $kernel"
+else
+	kernelrule="-bucket weightbucket"
+fi
+
 #Run your 3dsvm model
-3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D $maskrule -model model -bucket weightbucket $crossvrule
+3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D $maskrule -model model $kernelrule $crossvrule
 
 if [ "$totem" = "1" ] #delete your temporary totem files, if they existed
 then
@@ -128,7 +145,8 @@ then
 fi
 
 
+
 ##To add:
 #1) Model testing (on training data itself, be sure to use set detrend to no
 #2) Ability to automatically split examples into training and test set, and do cross validation randomly
-#3) Permutation tests (basically just a for loop with random permutation of labels file. Tricky thing is querying test model weights against giant population of permutation weights
\ No newline at end of file
+#3) Permutation tests (basically just a for loop with random permutation of labels file. Tricky thing is querying test model weights against giant population of permutation weights

From 6c58471d59c758956ab154b914c8410d7ff16802 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Fri, 2 Dec 2011 16:20:23 -0500
Subject: [PATCH 06/30] Added totem.suf (but currently dirty, contains examples
 of my data

---
 svmbatch/totem.suf | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 svmbatch/totem.suf

diff --git a/svmbatch/totem.suf b/svmbatch/totem.suf
new file mode 100644
index 00000000..54b5d447
--- /dev/null
+++ b/svmbatch/totem.suf
@@ -0,0 +1,2 @@
+/con_0003
+/con_0004

From b7d09489132097d815a79fb3ed2ef10bbf0ee4e5 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 12 Dec 2011 10:39:22 -0500
Subject: [PATCH 07/30] Updated options (and updated options support to default
 to more reasonable settings for older, non-totem and linear applications.

---
 svmbatch/svmbatch.sh | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index c919752b..85cc2dd1 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -44,7 +44,8 @@ while [ "$1" != "" ]; do
 			kernel=$1
 			echo Kernel specified is $kernel
 			;;
-	-d | --directory ) shift ; svmdir=$1
+	-d | --directory ) shift ; svmdir=$1;;
+	--nomodelmask ) nomodelmask=1;;
 			
     esac
     shift
@@ -117,13 +118,13 @@ done
 #Build a mask (in the future we may want to learn more about these options, or allow for specification of a custom mask
 3dAutomask timeshortbucket+orig
 
-#maskrule="-mask automask+orig"
-if [ "$totem" = "1" ]
+maskrule="-mask automask+orig"
+if [ "$totem" = "1" | "$nomodelmask" = "1" ]
 then
     maskrule="-nomodelmask"
 fi
 
-crossvrule="-x 1"
+crossvrule=""
 if [ "$crossv" = "1" ]
 then
     crossvrule="-x 1"

From b0b03344139d13d41dff8f4f96797ad1ce345269 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 12 Dec 2011 16:51:15 -0500
Subject: [PATCH 08/30] Huge rewrite. Everything in functional form now.
 Currently, main functionality is broken until it gets written back in.
 Hardcoded for crossval, which probably doesn't work anyway

---
 svmbatch/svmbatch.sh | 67 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 3 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 85cc2dd1..dc4747b2 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -24,6 +24,8 @@ function totembatch {
 }
 
 
+
+
 #Parameter Processing
 
 totem=
@@ -38,7 +40,8 @@ while [ "$1" != "" ]; do
 			#totemtemp=$1
 			echo Running in Totem Mode
 			;;
-	-c | --crossv )	crossv=1;; #Will perform cross validation
+	-c | --crossv )	crossv=1;; #Will perform cross validation per SVM-light
+	-C | --CROSSV ) scrossv=1;; #will do super cross validation (per dan)
 	-k | --kernel ) kernelmode=1 #Kernel has been specified
 			shift
 			kernel=$1
@@ -58,7 +61,7 @@ done
 
 #Read in variable values from associated files
 
-
+function svm_prep {
 
 filelist1=`cat filelist1`
 filelist2=`cat filelist2`
@@ -73,6 +76,12 @@ then
     mkdir $svmdir
 fi
 
+}
+
+
+
+function totem_build {
+
 #if in totem mode
 
 if [ "$totem" == 1 ]; 
@@ -86,6 +95,9 @@ if [ "$totem" == 1 ];
 
 
 fi
+}
+
+function afni_build{
 
 #Build bucket files out of each of your conditions
 3dbucket -sessiondir $svmdir -prefixname bucket1 $filelist1
@@ -102,7 +114,9 @@ cd $svmdir
 
 #Convert your short bucket to be of type "time" (required by 3dsvm)
 3dTcat -prefix timeshortbucket shortbucket+orig
+}
 
+function label_build {
 #Build filelist by appending 1s or 2s to label file based on number in each class category
 
 for i in $filelist1
@@ -114,10 +128,14 @@ for i in $filelist2
 do
 echo 2 >> labels.1D
 done
+}
 
+function mask_build {
 #Build a mask (in the future we may want to learn more about these options, or allow for specification of a custom mask
 3dAutomask timeshortbucket+orig
+}
 
+function setrules {
 maskrule="-mask automask+orig"
 if [ "$totem" = "1" | "$nomodelmask" = "1" ]
 then
@@ -136,15 +154,58 @@ then
 else
 	kernelrule="-bucket weightbucket"
 fi
+}
 
+function svm_train {
 #Run your 3dsvm model
-3dsvm -trainvol timeshortbucket+orig -trainlabels labels.1D $maskrule -model model $kernelrule $crossvrule
+3dsvm \
+-trainvol timeshortbucket+orig\
+-trainlabels labels.1D\ 
+$maskrule -model \
+model \
+$kernelrule \
+$crossvrule
 
 if [ "$totem" = "1" ] #delete your temporary totem files, if they existed
 then
     rm $totemtemp -rf
 fi
 
+}
+
+
+function main {
+svm_prep
+totem_build
+afni_build
+label_build
+mask_build
+setrules
+svm_train
+}
+
+#Super looper down here?
+
+#main #If nothing special, just run it I guess?
+
+svmdir_orig=echo $svmdir
+filelist1_orig=echo "$filelist1"
+filelist2_orig=echo "$filelist2"
+
+biglist=`cat filelist1 filelist2`
+for file in $biglist
+do
+filename=`cat $file | sed -e 's:/:_:2g' `
+svmdir= echo $svmdir/$filename
+filelist1=`echo "$filelist1" | sed "/$file/ d" `
+filelist2=`echo "$filelist2" | sed "/$file/ d" `
+
+totem_build
+afni_build
+label_build
+mask_build
+setrules
+svm_train
 
 
 ##To add:

From b286e6acb8fd113083ba87d05584e7619d8116ea Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Tue, 13 Dec 2011 11:26:40 -0500
Subject: [PATCH 09/30] Cleaned up functional rewrite

---
 svmbatch/svmbatch.sh | 134 +++++++++++++++++++++++++------------------
 1 file changed, 77 insertions(+), 57 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index dc4747b2..77dd9c81 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -10,17 +10,17 @@ function totembatch {
     #Given a filelist, suffixlist, and totem directory, loop over
     #combinations of filelist and suffixlist, and build totems
 
-    totemsuf=`cat totem.suf`
-    
-    for  file in $1; do
-	totemlist=  #Clear the totemlist variable. This will hold the list of all the subfiles going into your totem
-	for suf in $totemsuf; do
-		totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
-	done
-	newname=`echo $file | sed 's:/:_:2g'` #edit the filename to have underscores instead of slashes, it will keep the temp directory cleaner
-	fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
-	newname=
+totemsuf=`cat totem.suf`
+
+for  file in $1; do
+    totemlist=  #Clear the totemlist variable. This will hold the list of all the subfiles going into your totem
+    for suf in $totemsuf; do
+	totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
     done
+    newname=`echo $file | sed 's:/:_:2g'` #edit the filename to have underscores instead of slashes, it will keep the temp directory cleaner
+    fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
+    newname=
+done
 }
 
 
@@ -33,27 +33,42 @@ crossv=
 totemtemp=/tmp/totems #Where to store your totem files/examples
 
 
+
+
+
+
 while [ "$1" != "" ]; do
     case $1 in
-	-t | --totem )	totem=1  #Operate in totem stacking mode
-			#shift
-			#totemtemp=$1
-			echo Running in Totem Mode
-			;;
-	-c | --crossv )	crossv=1;; #Will perform cross validation per SVM-light
-	-C | --CROSSV ) scrossv=1;; #will do super cross validation (per dan)
-	-k | --kernel ) kernelmode=1 #Kernel has been specified
-			shift
-			kernel=$1
-			echo Kernel specified is $kernel
-			;;
-	-d | --directory ) shift ; svmdir=$1;;
-	--nomodelmask ) nomodelmask=1;;
-			
+	-t | --totem )
+	    totem=1  #Operate in totem stacking mode
+	    #shift
+	    #totemtemp=$1
+	    echo Running in Totem Mode
+	    ;;
+	-c | --crossv )	
+	    crossv=1
+	    ;; #Will perform cross validation per SVM-light
+	-C | --CROSSV ) 
+	    scrossv=1
+	    ;; #will do super cross validation (per dan)
+	-k | --kernel ) 
+	    kernelmode=1 #Kernel has been specified
+	    shift
+	    kernel=$1
+	    echo Kernel specified is $kernel
+	    ;;
+	-d | --directory )
+	    shift
+	    svmdir=$1
+	    ;;
+	--nomodelmask ) 
+	    nomodelmask=1
+	    ;;
+
     esac
     shift
 done
-       
+
 
 ##Main Function
 
@@ -67,12 +82,12 @@ filelist1=`cat filelist1`
 filelist2=`cat filelist2`
 
 if [ -f svmdir ]
-then
+    then
     svmdir=`cat svmdir`
 fi
 
 if [ ! -d $svmdir ]
-then
+    then
     mkdir $svmdir
 fi
 
@@ -84,7 +99,7 @@ function totem_build {
 
 #if in totem mode
 
-if [ "$totem" == 1 ]; 
+if [ "$totem" == 1 ];
     then
     mkdir $totemtemp
     totembatch "$filelist1"
@@ -120,13 +135,13 @@ function label_build {
 #Build filelist by appending 1s or 2s to label file based on number in each class category
 
 for i in $filelist1
-do
-echo 1 >>labels.1D
+  do
+  echo 1 >>labels.1D
 done
 
 for i in $filelist2
-do
-echo 2 >> labels.1D
+  do
+  echo 2 >> labels.1D
 done
 }
 
@@ -138,36 +153,36 @@ function mask_build {
 function setrules {
 maskrule="-mask automask+orig"
 if [ "$totem" = "1" | "$nomodelmask" = "1" ]
-then
+    then
     maskrule="-nomodelmask"
 fi
 
 crossvrule=""
 if [ "$crossv" = "1" ]
-then
+    then
     crossvrule="-x 1"
 fi
 
 if [ "$kernelmode" = "1" ] #if running in kernel mode
-then
-	kernelrule="-kernel $kernel"
+    then
+    kernelrule="-kernel $kernel"
 else
-	kernelrule="-bucket weightbucket"
+    kernelrule="-bucket weightbucket"
 fi
 }
 
 function svm_train {
 #Run your 3dsvm model
 3dsvm \
--trainvol timeshortbucket+orig\
--trainlabels labels.1D\ 
+    -trainvol timeshortbucket+orig\
+    -trainlabels labels.1D\
 $maskrule -model \
-model \
-$kernelrule \
-$crossvrule
+    model \
+    $kernelrule \
+    $crossvrule
 
 if [ "$totem" = "1" ] #delete your temporary totem files, if they existed
-then
+    then
     rm $totemtemp -rf
 fi
 
@@ -194,20 +209,25 @@ filelist2_orig=echo "$filelist2"
 
 biglist=`cat filelist1 filelist2`
 for file in $biglist
-do
-filename=`cat $file | sed -e 's:/:_:2g' `
-svmdir= echo $svmdir/$filename
-filelist1=`echo "$filelist1" | sed "/$file/ d" `
-filelist2=`echo "$filelist2" | sed "/$file/ d" `
-
-totem_build
-afni_build
-label_build
-mask_build
-setrules
-svm_train
-
+  do
+  curdir=`echo $file | sed -e 's:/:_:2g' `
+  svmdir= echo $svmdir/$curdir
+  filelist1=`echo "$filelist1" | sed "/$file/ d" `
+  filelist2=`echo "$filelist2" | sed "/$file/ d" `
+  
+  echo "$svmdir"
+  echo "$filelist1"
+  echo "$filelist2"
+
+#   totem_build
+#   afni_build
+#   label_build
+#   mask_build
+#   setrules
+#   svm_train
+done
 
+  
 ##To add:
 #1) Model testing (on training data itself, be sure to use set detrend to no
 #2) Ability to automatically split examples into training and test set, and do cross validation randomly

From f27a9ab87b5857d14403dd424a44e06b2dd033ac Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 12:38:19 -0500
Subject: [PATCH 10/30] Huge functional rewrite of svmbatch code

---
 svmbatch/svmbatch.sh | 216 +++++++++++++++++++++++++++++++------------
 1 file changed, 157 insertions(+), 59 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 77dd9c81..65993e0d 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -4,24 +4,6 @@
 
 #CONSTANTS
 
-#FUNCTIONS
-
-function totembatch {
-    #Given a filelist, suffixlist, and totem directory, loop over
-    #combinations of filelist and suffixlist, and build totems
-
-totemsuf=`cat totem.suf`
-
-for  file in $1; do
-    totemlist=  #Clear the totemlist variable. This will hold the list of all the subfiles going into your totem
-    for suf in $totemsuf; do
-	totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
-    done
-    newname=`echo $file | sed 's:/:_:2g'` #edit the filename to have underscores instead of slashes, it will keep the temp directory cleaner
-    fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
-    newname=
-done
-}
 
 
 
@@ -70,13 +52,61 @@ while [ "$1" != "" ]; do
 done
 
 
-##Main Function
 
 
+#FUNCTIONS
+
+function totem_build { #
+
+#if in totem mode
+
+if [ "$totem" == 1 ];
+    then
+    mkdir $totemtemp
+    totembatch "$filelist1"
+    totembatch "$filelist2"
+
+    filelist1= `hdr_append  `prepend $totemtemp  `slash_strip "$filelist1"` ` `
+    filelist2= `hdr_append  `prepend $totemtemp  `slash_strip "$filelist2"` ` `
+
+    #filelist1=`cat filelist1 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'` #Update the filelist to point to where the totem-ed files are
+    #filelist2=`cat filelist2 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'`
+
+
+fi
+}
+
+function totembatch { #Read totem.suf, mk totemtemp, assemble totems, update filelist to point to totems
+
+totemsuf=`cat totem.suf`
+
+mkdir $totemtemp
+
+function totem_build {
+
+for  file in $1; do
+    totemlist=  #Clear totemlist. Holds names of files to go into totem
+    newname= #Clear newname. Holds name of target totem
+    for suf in $totemsuf; do
+	totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
+    done
+    newname=`slash_strip $file`
+    fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
+    newname=
+done
+}
+
+totem_build $filelist1 #Quoting doesn't matter here for list ops
+totem_build $filelist2 #And function will not quote anyway
+
+filelist1=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist1" \\\` \` `
+filelist2=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist2" \\\` \` `
+}
+
 
 #Read in variable values from associated files
 
-function svm_prep {
+function svm_prep { #Read in filelists, svmdir, totem.suf and make svmdir
 
 filelist1=`cat filelist1`
 filelist2=`cat filelist2`
@@ -91,31 +121,84 @@ if [ ! -d $svmdir ]
     mkdir $svmdir
 fi
 
+if [ "$totem" = "1" ]; thhen    totemlist=  #Clear the totemlist variable. This will hold the list of all the subfiles going into your totem
+    for suf in $totemsuf;
+      do
+      totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
+    done
+    newname=`echo $file | sed 's:/:_:2g'` #edit the filename to have underscores instead of slashes, it will keep the temp directory cleaner
+    fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
+    newname=
+    done
 }
 
 
+#Read in variable values from associated files
 
-function totem_build {
+function svm_prep { #Read in filelists, svmdir, and make svmdir
 
-#if in totem mode
+filelist1=`cat filelist1`
+filelist2=`cat filelist2`
 
-if [ "$totem" == 1 ];
+if [ -f svmdir ]
     then
-    mkdir $totemtemp
-    totembatch "$filelist1"
-    totembatch "$filelist2"
+    svmdir=`cat svmdir`
+fi
 
-    filelist1=`cat filelist1 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'` #Update the filelist to point to where the totem-ed files are
-    filelist2=`cat filelist2 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'`
+if [ ! -d $svmdir ]
+    then
+    mkdir $svmdir
+fi
 
 
-fi
+
+}
+
+function slash_strip { #Strip all slashes off $1,prepend slash 
+echo "$1" | sed -e 's:/:_:g' -e 's:^:/:'
+}
+
+function prepend { #Will prepend $1 to all of $2
+echo "$2" | sed "s:^:/$1:"
+}
+
+function hdr_append { #Add .hdr to end of $1
+echo "$1" | sed "s:$:.hdr:"
+}
+
+function hdr_strip { #Remove all instances of .hdr from $1
+echo "$1" | sed "s:.hdr::"
+}
+
+function afni_bucket_build { #Build converted bucket files from list $1
+3dbucket -sessiondir $svmdir -prefixname bucket$2 $1
+}
+
+function afni_bucket_combine { #Combine buckets specified in $1, name them $2
+cd $svmdir
+
+bucketlist=
+for bucket in $1; do
+    bucketlist=`echo $bucketlist $bucket+orig `
+done
+
+3dbucket -prefixname $2 $bucketlist
+}
+
+function afni_bucket_short { #Convert bucket specified in $1 to short, named by $2
+cd $svmdir
+3dcalc -a $1+orig -expr "a" -prefixname $2 -datum short
+}
+
+function afni_bucket_time { #convert bucket in $1 to be of type time, named $2
+cd $svmdir
+3dTcat -prefix $2 $1+orig
 }
 
-function afni_build{
+function afni_build { #Build bucket files from list in $1, name suf $2 (convert, combine, calc, timeify)
 
 #Build bucket files out of each of your conditions
-3dbucket -sessiondir $svmdir -prefixname bucket1 $filelist1
+3dbucket -sessiondir $svmdir -prefixname bucket$2 $1
 3dbucket -sessiondir $svmdir -prefixname bucket2 $filelist2
 
 #Change to the svm working directory (presumably where this script was called from)
@@ -131,8 +214,7 @@ cd $svmdir
 3dTcat -prefix timeshortbucket shortbucket+orig
 }
 
-function label_build {
-#Build filelist by appending 1s or 2s to label file based on number in each class category
+function label_build { #Make label file
 
 for i in $filelist1
   do
@@ -145,49 +227,59 @@ for i in $filelist2
 done
 }
 
-function mask_build {
-#Build a mask (in the future we may want to learn more about these options, or allow for specification of a custom mask
+function mask_build { #Build automask
 3dAutomask timeshortbucket+orig
 }
 
-function setrules {
+function set_train_rules { #Set rules for 3dsvm training based on options
 maskrule="-mask automask+orig"
-if [ "$totem" = "1" | "$nomodelmask" = "1" ]
-    then
+if [ "$totem" = "1" | "$nomodelmask" = "1" ]; then
     maskrule="-nomodelmask"
 fi
 
 crossvrule=""
-if [ "$crossv" = "1" ]
-    then
+if [ "$crossv" = "1" ]; then
     crossvrule="-x 1"
 fi
 
-if [ "$kernelmode" = "1" ] #if running in kernel mode
-    then
+kernelrule="-bucket weightbucket"
+if [ "$kernelmode" = "1" ]; then #if running in kernel mode
     kernelrule="-kernel $kernel"
-else
-    kernelrule="-bucket weightbucket"
 fi
 }
 
-function svm_train {
+function svm_train { #Train on timeshort labeled in $1
 #Run your 3dsvm model
 3dsvm \
-    -trainvol timeshortbucket+orig\
+    -trainvol $1+orig\
     -trainlabels labels.1D\
-$maskrule -model \
+    $maskrule -model \
     model \
     $kernelrule \
     $crossvrule
 
-if [ "$totem" = "1" ] #delete your temporary totem files, if they existed
+}
+
+function totem_clean { #delete your temporary totem files, if they existed
+if [ "$totem" = "1" ] 
     then
     rm $totemtemp -rf
 fi
 
 }
 
+function set_test_rules { #Set rules for 3dsvm testing based on options
+
+function svm_test { #Test model #1 against volume #2
+3dsvm \
+    -model $1 \
+    -testvol $2 \
+    -predictions $pname\
+    -nodetrend
+
+}
+
+
 
 function main {
 svm_prep
@@ -199,25 +291,30 @@ setrules
 svm_train
 }
 
+
+
 #Super looper down here?
 
 #main #If nothing special, just run it I guess?
 
-svmdir_orig=echo $svmdir
-filelist1_orig=echo "$filelist1"
-filelist2_orig=echo "$filelist2"
+svm_prep
+
+svmdir_orig=$svmdir
+filelist1_orig="$filelist1"
+filelist2_orig="$filelist2"
+
 
-biglist=`cat filelist1 filelist2`
+biglist=`echo -e "$filelist1\n$filelist1"` #Concatenate your two lists
 for file in $biglist
   do
-  curdir=`echo $file | sed -e 's:/:_:2g' `
-  svmdir= echo $svmdir/$curdir
-  filelist1=`echo "$filelist1" | sed "/$file/ d" `
-  filelist2=`echo "$filelist2" | sed "/$file/ d" `
+  curdir=`hdr_strip \`slash_strip $file \` `
+  svmdir=`echo $svmdir_orig/$curdir`	
+  filelist1=`echo "$filelist1" | sed "\:$file: d" ` #Because our $file has tons of slashes, we use : as the delimeter
+  filelist2=`echo "$filelist2" | sed "\:$file: d" `
   
   echo "$svmdir"
-  echo "$filelist1"
-  echo "$filelist2"
+#  echo "$filelist1"
+ # echo "$filelist2"
 
 #   totem_build
 #   afni_build
@@ -227,8 +324,9 @@ for file in $biglist
 #   svm_train
 done
 
-  
+
 ##To add:
 #1) Model testing (on training data itself, be sure to use set detrend to no
 #2) Ability to automatically split examples into training and test set, and do cross validation randomly
 #3) Permutation tests (basically just a for loop with random permutation of labels file. Tricky thing is querying test model weights against giant population of permutation weights
+

From 90c39931e7eed40d2b712a5309d72412353e8580 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 12:05:06 -0500
Subject: [PATCH 11/30] More updates. About to start testing

---
 svmbatch/svmbatch.sh | 171 +++++++++++++++----------------------------
 1 file changed, 58 insertions(+), 113 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 65993e0d..b5f63f8e 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -15,10 +15,6 @@ crossv=
 totemtemp=/tmp/totems #Where to store your totem files/examples
 
 
-
-
-
-
 while [ "$1" != "" ]; do
     case $1 in
 	-t | --totem )
@@ -56,34 +52,11 @@ done
 
 #FUNCTIONS
 
-function totem_build { #
-
-#if in totem mode
-
-if [ "$totem" == 1 ];
-    then
-    mkdir $totemtemp
-    totembatch "$filelist1"
-    totembatch "$filelist2"
-
-    filelist1= `hdr_append  `prepend $totemtemp  `slash_strip "$filelist1"` ` `
-    filelist2= `hdr_append  `prepend $totemtemp  `slash_strip "$filelist2"` ` `
-
-    #filelist1=`cat filelist1 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'` #Update the filelist to point to where the totem-ed files are
-    #filelist2=`cat filelist2 | sed -e 's:/:_:2g' -e 's:^:/'$totemtemp: -e 's:$:.hdr:'`
-
-
-fi
-}
 
 function totembatch { #Read totem.suf, mk totemtemp, assemble totems, update filelist to point to totems
-
 totemsuf=`cat totem.suf`
-
 mkdir $totemtemp
-
 function totem_build {
-
 for  file in $1; do
     totemlist=  #Clear totemlist. Holds names of files to go into totem
     newname= #Clear newname. Holds name of target totem
@@ -95,63 +68,23 @@ for  file in $1; do
     newname=
 done
 }
-
 totem_build $filelist1 #Quoting doesn't matter here for list ops
 totem_build $filelist2 #And function will not quote anyway
-
-filelist1=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist1" \\\` \` `
+filelist1=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist1" \\\` \` ` #update names to point at totems
 filelist2=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist2" \\\` \` `
 }
 
 
-#Read in variable values from associated files
-
-function svm_prep { #Read in filelists, svmdir, totem.suf and make svmdir
-
-filelist1=`cat filelist1`
-filelist2=`cat filelist2`
-
-if [ -f svmdir ]
-    then
-    svmdir=`cat svmdir`
-fi
-
-if [ ! -d $svmdir ]
-    then
-    mkdir $svmdir
-fi
-
-if [ "$totem" = "1" ]; thhen    totemlist=  #Clear the totemlist variable. This will hold the list of all the subfiles going into your totem
-    for suf in $totemsuf;
-      do
-      totemlist=`echo $totemlist $file/$suf` #loop over suffixes, and build up the list of subfiles
-    done
-    newname=`echo $file | sed 's:/:_:2g'` #edit the filename to have underscores instead of slashes, it will keep the temp directory cleaner
-    fslmerge -z $totemtemp/$newname $totemlist  #use fsl to merge your subfiles in the z direction into totems
-    newname=
-    done
-}
-
-
-#Read in variable values from associated files
-
 function svm_prep { #Read in filelists, svmdir, and make svmdir
-
 filelist1=`cat filelist1`
 filelist2=`cat filelist2`
-
-if [ -f svmdir ]
-    then
+if [ -f svmdir ]; then
     svmdir=`cat svmdir`
 fi
 
-if [ ! -d $svmdir ]
-    then
+if [ ! -d $svmdir ]; then
     mkdir $svmdir
 fi
-
-
-
 }
 
 function slash_strip { #Strip all slashes off $1,prepend slash 
@@ -170,8 +103,8 @@ function hdr_strip { #Remove all instances of .hdr from $1
 echo "$1" | sed "s:.hdr::"
 }
 
-function afni_bucket_build { #Build converted bucket files from list $1
-3dbucket -sessiondir $svmdir -prefixname bucket$2 $1
+function afni_bucket_build { #Build converted bucket files from list $1, named $2
+3dbucket -sessiondir $svmdir -prefixname $2 $1
 }
 
 function afni_bucket_combine { #Combine buckets specified in $1, name them $2
@@ -251,15 +184,27 @@ fi
 function svm_train { #Train on timeshort labeled in $1
 #Run your 3dsvm model
 3dsvm \
-    -trainvol $1+orig\
-    -trainlabels labels.1D\
-    $maskrule -model \
-    model \
+    -trainvol $1+orig \
+    -trainlabels labels.1D \
+    $maskrule \
+    -model  model \
     $kernelrule \
     $crossvrule
 
 }
 
+function svm_batchtrain { #Based on curval of $filelists and $svmdir, does all the lifting
+afni_bucket_build "$filelist1" "bucket1"
+afni_bucket_build "$filelist2" "bucket2"
+afni_bucket_combine "bucket1 bucket2" "bucket"
+afni_bucket_short "bucket" "bucketshort"
+afni_bucket_time "bucketshort" "bucketshorttime"
+label_build
+set_train_rules
+svm_train "bucketshorttime"
+}
+
+
 function totem_clean { #delete your temporary totem files, if they existed
 if [ "$totem" = "1" ] 
     then
@@ -269,60 +214,60 @@ fi
 }
 
 function set_test_rules { #Set rules for 3dsvm testing based on options
+echo You need to finish this one Dan
+}
 
-function svm_test { #Test model #1 against volume #2
+function svm_test { #Test model $1 against volume $2
 3dsvm \
-    -model $1 \
-    -testvol $2 \
+    -model $1+orig \
+    -testvol $2+orig \
     -predictions $pname\
     -nodetrend
 
 }
 
+function svm_batchtest { #Test model $1 against constructed volume based on hdrs in $2
+afni_bucket_build "$1" "testbucket"
+afni_bucket_short "testbucket" "testbucketshort"
+afni_bucket_time "testbucketshort" "testbucketshorttime"
+set_test_rukes
+svm_test $1 "testbucketshorttime"
+}
 
+function super_crossvalid { #no arguments. Performs LOO-CV manually, and saved predictions
+svmdir_orig=$svmdir
+filelist1_orig=$filelist1
+filelist2_orig=$filelist2
+
+biglist=`echo -e "$filelist1\n$filelist2"`
+for file in $filelist; do
+    echo "Now working on LOOCV for $file"
+    pname="pred" #this is the file predictions will get written to. file specific will be better
+    loodir=`hdr_strip \`slash_strip $file \` ` #Make file into a dirname
+    svmdir=`echo $svmdir_orig/LOOCV/$loodir   ` #build a dir from loodir and svmdir_orig
+    filelist1=`echo "$filelist1" | sed "\:$file: d" ` #remove $file from filelist1
+    filelist2=`echo "$filelist2" | sed "\:$file: d" ` #remove $file from filelist2
+    svm_batchtrain #train up a model based on the updated filelist and svmdir
+    svm_batchtest "model" "$file"
+done
 
 function main {
 svm_prep
 totem_build
-afni_build
-label_build
-mask_build
-setrules
-svm_train
-}
-
 
+if [ "$CROSSV" != "1" ]; then
+    echo "Training one and only model"
+    svm_batchtrain
+else
+    echo "Entering Super Cross Validation Mode!"
+    super_crossvalid
+fi
 
-#Super looper down here?
-
-#main #If nothing special, just run it I guess?
-
-svm_prep
+}
 
-svmdir_orig=$svmdir
-filelist1_orig="$filelist1"
-filelist2_orig="$filelist2"
 
+main
 
-biglist=`echo -e "$filelist1\n$filelist1"` #Concatenate your two lists
-for file in $biglist
-  do
-  curdir=`hdr_strip \`slash_strip $file \` `
-  svmdir=`echo $svmdir_orig/$curdir`	
-  filelist1=`echo "$filelist1" | sed "\:$file: d" ` #Because our $file has tons of slashes, we use : as the delimeter
-  filelist2=`echo "$filelist2" | sed "\:$file: d" `
-  
-  echo "$svmdir"
-#  echo "$filelist1"
- # echo "$filelist2"
-
-#   totem_build
-#   afni_build
-#   label_build
-#   mask_build
-#   setrules
-#   svm_train
-done
 
 
 ##To add:

From 3abb1cef8b27f298d84ba2995a5cca3ca30a195d Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 12:27:01 -0500
Subject: [PATCH 12/30] Testing completed on new functional form

---
 svmbatch/svmbatch.sh | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index b5f63f8e..bdea64b9 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -49,7 +49,6 @@ done
 
 
 
-
 #FUNCTIONS
 
 
@@ -104,7 +103,7 @@ echo "$1" | sed "s:.hdr::"
 }
 
 function afni_bucket_build { #Build converted bucket files from list $1, named $2
-3dbucket -sessiondir $svmdir -prefixname $2 $1
+3dbucket -sessiondir $svmdir -prefixname $2 $1 2>/dev/null
 }
 
 function afni_bucket_combine { #Combine buckets specified in $1, name them $2
@@ -166,7 +165,7 @@ function mask_build { #Build automask
 
 function set_train_rules { #Set rules for 3dsvm training based on options
 maskrule="-mask automask+orig"
-if [ "$totem" = "1" | "$nomodelmask" = "1" ]; then
+if [ "$totem" = "1" -o "$nomodelmask" = "1" ]; then
     maskrule="-nomodelmask"
 fi
 
@@ -227,7 +226,7 @@ function svm_test { #Test model $1 against volume $2
 }
 
 function svm_batchtest { #Test model $1 against constructed volume based on hdrs in $2
-afni_bucket_build "$1" "testbucket"
+afni_bucket_build "$2" "testbucket"
 afni_bucket_short "testbucket" "testbucketshort"
 afni_bucket_time "testbucketshort" "testbucketshorttime"
 set_test_rukes
@@ -239,23 +238,34 @@ svmdir_orig=$svmdir
 filelist1_orig=$filelist1
 filelist2_orig=$filelist2
 
+mkdir $svmdir_orig/LOOCV/
+
 biglist=`echo -e "$filelist1\n$filelist2"`
-for file in $filelist; do
+for file in $biglist; do
     echo "Now working on LOOCV for $file"
-    pname="pred" #this is the file predictions will get written to. file specific will be better
+    pname="$file" #this is the file predictions will get written to. file specific will be better
     loodir=`hdr_strip \`slash_strip $file \` ` #Make file into a dirname
+    pname=`echo "$loodir" | sed 's:/::'`
     svmdir=`echo $svmdir_orig/LOOCV/$loodir   ` #build a dir from loodir and svmdir_orig
     filelist1=`echo "$filelist1" | sed "\:$file: d" ` #remove $file from filelist1
     filelist2=`echo "$filelist2" | sed "\:$file: d" ` #remove $file from filelist2
     svm_batchtrain #train up a model based on the updated filelist and svmdir
     svm_batchtest "model" "$file"
 done
+}
 
 function main {
 svm_prep
+
+if [ "$totem" = "1" ]; then
+    
 totem_build
+    
+fi
+
+
 
-if [ "$CROSSV" != "1" ]; then
+if [ "$scrossv" != "1" ]; then
     echo "Training one and only model"
     svm_batchtrain
 else

From 2ae54f237fde4d42895534452eaab53bfbbd084f Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 13:07:41 -0500
Subject: [PATCH 13/30] Removed dirty lines from sample totem.suf

---
 svmbatch/totem.suf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/svmbatch/totem.suf b/svmbatch/totem.suf
index 54b5d447..e69de29b 100644
--- a/svmbatch/totem.suf
+++ b/svmbatch/totem.suf
@@ -1,2 +0,0 @@
-/con_0003
-/con_0004

From 41042786ab2e0c754a953eda0bf9fed65241d56c Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 13:12:34 -0500
Subject: [PATCH 14/30] Fixed errors around totem mode

---
 svmbatch/svmbatch.sh | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index bdea64b9..494a7b99 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -52,7 +52,7 @@ done
 #FUNCTIONS
 
 
-function totembatch { #Read totem.suf, mk totemtemp, assemble totems, update filelist to point to totems
+function totem_batch { #Read totem.suf, mk totemtemp, assemble totems, update filelist to point to totems
 totemsuf=`cat totem.suf`
 mkdir $totemtemp
 function totem_build {
@@ -259,7 +259,7 @@ svm_prep
 
 if [ "$totem" = "1" ]; then
     
-totem_build
+totem_batch
     
 fi
 
@@ -273,6 +273,12 @@ else
     super_crossvalid
 fi
 
+if [ "$totem" = "1" ]; then
+    
+totem_clean
+    
+fi
+
 }
 
 

From 7e27b7ac06482acc32cbdb78275cfa0a77994b9e Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 14:04:19 -0500
Subject: [PATCH 15/30] Fixed issues with totem processor (mostly quoting
 problems). Fixed one small typo that had no present impact, but may if we use
 "test rules" in the future

---
 svmbatch/svmbatch.sh | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 494a7b99..807ca122 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -56,7 +56,7 @@ function totem_batch { #Read totem.suf, mk totemtemp, assemble totems, update fi
 totemsuf=`cat totem.suf`
 mkdir $totemtemp
 function totem_build {
-for  file in $1; do
+  for  file in $1; do
     totemlist=  #Clear totemlist. Holds names of files to go into totem
     newname= #Clear newname. Holds name of target totem
     for suf in $totemsuf; do
@@ -67,10 +67,18 @@ for  file in $1; do
     newname=
 done
 }
-totem_build $filelist1 #Quoting doesn't matter here for list ops
-totem_build $filelist2 #And function will not quote anyway
-filelist1=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist1" \\\` \` ` #update names to point at totems
-filelist2=`hdr_append \`prepend $totemtemp \\\`slash_strip "$filelist2" \\\` \` `
+totem_build "$filelist1" #Quoting here DOES matter. Otherwise it will take only first element as $1
+totem_build "$filelist2"
+
+
+filelist1=`slash_strip "$filelist1"`
+filelist1=`prepend $totemtemp "$filelist1"`
+filelist1=`hdr_append "$filelist1"`
+
+filelist2=`slash_strip "$filelist2"`
+filelist2=`prepend $totemtemp "$filelist2"`
+filelist2=`hdr_append "$filelist2"`
+
 }
 
 
@@ -229,7 +237,7 @@ function svm_batchtest { #Test model $1 against constructed volume based on hdrs
 afni_bucket_build "$2" "testbucket"
 afni_bucket_short "testbucket" "testbucketshort"
 afni_bucket_time "testbucketshort" "testbucketshorttime"
-set_test_rukes
+set_test_rules
 svm_test $1 "testbucketshorttime"
 }
 

From 985372efca7ea44532e36e80d506d90d4a773804 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 14 Dec 2011 14:13:50 -0500
Subject: [PATCH 16/30] Fixed mistake in super cross validation that
 PROGRESSIVELY eliminated cases, rather than doing so with replacement after
 each LOOCV

---
 svmbatch/svmbatch.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 807ca122..4cca195a 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -255,8 +255,8 @@ for file in $biglist; do
     loodir=`hdr_strip \`slash_strip $file \` ` #Make file into a dirname
     pname=`echo "$loodir" | sed 's:/::'`
     svmdir=`echo $svmdir_orig/LOOCV/$loodir   ` #build a dir from loodir and svmdir_orig
-    filelist1=`echo "$filelist1" | sed "\:$file: d" ` #remove $file from filelist1
-    filelist2=`echo "$filelist2" | sed "\:$file: d" ` #remove $file from filelist2
+    filelist1=`echo "$filelist1_orig" | sed "\:$file: d" ` #remove $file from filelist1
+    filelist2=`echo "$filelist2_orig" | sed "\:$file: d" ` #remove $file from filelist2
     svm_batchtrain #train up a model based on the updated filelist and svmdir
     svm_batchtest "model" "$file"
 done

From 2945dec6221d2b6339276ff9df51800ed89d81ef Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Fri, 16 Dec 2011 17:20:04 -0500
Subject: [PATCH 17/30] Added tentative support for permutation testing

---
 svmbatch/svmbatch.sh | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 4cca195a..76edfe10 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -42,6 +42,9 @@ while [ "$1" != "" ]; do
 	--nomodelmask ) 
 	    nomodelmask=1
 	    ;;
+	-p | --permutation )
+	    permutationmode=1
+	    ;;
 
     esac
     shift
@@ -167,6 +170,10 @@ for i in $filelist2
 done
 }
 
+function label_permute { #Randomly permute the labels in a given label file
+for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]+//' > $1
+}
+
 function mask_build { #Build automask
 3dAutomask timeshortbucket+orig
 }
@@ -207,6 +214,9 @@ afni_bucket_combine "bucket1 bucket2" "bucket"
 afni_bucket_short "bucket" "bucketshort"
 afni_bucket_time "bucketshort" "bucketshorttime"
 label_build
+if [ "$permute" = "1" ]; then
+    label_permute labels.1D
+fi
 set_train_rules
 svm_train "bucketshorttime"
 }
@@ -262,6 +272,16 @@ for file in $biglist; do
 done
 }
 
+function permutation_test { #will perfrom $1 permutations on data, writing out weight buckets at each step
+permute=1
+for i in `seq 1 $1`; do
+svmdir=`echo svmdir/perm$i`
+svm_batchtrain
+done
+
+}
+
+
 function main {
 svm_prep
 
@@ -281,6 +301,10 @@ else
     super_crossvalid
 fi
 
+if [ "$permutationmode" = "1" ]; then
+    echo "Entering permutation mode"
+    sbm_batchtrain
+
 if [ "$totem" = "1" ]; then
     
 totem_clean

From 92f3fe998ba57428abf15f7d5a08ca15cac588f2 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Fri, 16 Dec 2011 17:33:35 -0500
Subject: [PATCH 18/30] hopefully fixed permutation test errors

---
 svmbatch/svmbatch.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 76edfe10..b3042370 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -275,7 +275,8 @@ done
 function permutation_test { #will perfrom $1 permutations on data, writing out weight buckets at each step
 permute=1
 for i in `seq 1 $1`; do
-svmdir=`echo svmdir/perm$i`
+echo "Running permutation $i of $1"
+svmdir=`echo $svmdir/perms/$i`
 svm_batchtrain
 done
 
@@ -303,7 +304,8 @@ fi
 
 if [ "$permutationmode" = "1" ]; then
     echo "Entering permutation mode"
-    sbm_batchtrain
+    svm_batchtrain
+fi
 
 if [ "$totem" = "1" ]; then
     

From b13d8aeb89492896f8d040b99771aad646fba632 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 09:48:53 -0500
Subject: [PATCH 19/30] Permutation testing is now working. Planning to use
 symlinks for next release to speed up processing

---
 svmbatch/svmbatch.sh | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index b3042370..4c248d97 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -95,6 +95,11 @@ fi
 if [ ! -d $svmdir ]; then
     mkdir $svmdir
 fi
+
+filelist1_orig="$filelist1"
+filelist2_orig="$filelist2"
+svmdir_orig="$svmdir"
+
 }
 
 function slash_strip { #Strip all slashes off $1,prepend slash 
@@ -171,7 +176,9 @@ done
 }
 
 function label_permute { #Randomly permute the labels in a given label file
-for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]+//' > $1
+for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]+//' > plabels.1D
+rm labels.1D
+mv plabels.1D labels.1D
 }
 
 function mask_build { #Build automask
@@ -215,6 +222,7 @@ afni_bucket_short "bucket" "bucketshort"
 afni_bucket_time "bucketshort" "bucketshorttime"
 label_build
 if [ "$permute" = "1" ]; then
+    cd $svmdir
     label_permute labels.1D
 fi
 set_train_rules
@@ -274,9 +282,11 @@ done
 
 function permutation_test { #will perfrom $1 permutations on data, writing out weight buckets at each step
 permute=1
+mkdir $svmdir/perms
 for i in `seq 1 $1`; do
 echo "Running permutation $i of $1"
-svmdir=`echo $svmdir/perms/$i`
+svmdir=`echo $svmdir_orig/perms/$i`
+mkdir $svmdir
 svm_batchtrain
 done
 
@@ -304,7 +314,7 @@ fi
 
 if [ "$permutationmode" = "1" ]; then
     echo "Entering permutation mode"
-    svm_batchtrain
+    permutation_test 100
 fi
 
 if [ "$totem" = "1" ]; then

From 6c7c26ca1a656c2b6d86fd1f5556be39575435a1 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 09:53:40 -0500
Subject: [PATCH 20/30] Updated permutation test to leverage preexisting
 training examples through symlinks

---
 svmbatch/svmbatch.sh | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index 4c248d97..fe3e58f3 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -176,7 +176,7 @@ done
 }
 
 function label_permute { #Randomly permute the labels in a given label file
-for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]+//' > plabels.1D
+for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]\s+//' > plabels.1D
 rm labels.1D
 mv plabels.1D labels.1D
 }
@@ -287,9 +287,13 @@ for i in `seq 1 $1`; do
 echo "Running permutation $i of $1"
 svmdir=`echo $svmdir_orig/perms/$i`
 mkdir $svmdir
-svm_batchtrain
+cd $svmdir
+ln -s $svmdir_orig/bucketshorttime* .
+cp $svmdir_orig/labels.1D ./labels.1D
+label_permute labels.1D
+set_train_rules
+svm_train "bucketshorttime"
 done
-
 }
 
 

From f78e0d87f35ed29b716754f51142768f75c33dd6 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 10:03:11 -0500
Subject: [PATCH 21/30] Added support for specifying count of permutation tests
 at command line

---
 svmbatch/svmbatch.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index fe3e58f3..d46ffa5f 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -44,6 +44,8 @@ while [ "$1" != "" ]; do
 	    ;;
 	-p | --permutation )
 	    permutationmode=1
+	    shift
+	    permcount=$1
 	    ;;
 
     esac
@@ -176,7 +178,7 @@ done
 }
 
 function label_permute { #Randomly permute the labels in a given label file
-for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]\s+//' > plabels.1D
+for i in `cat $1`; do echo "$RANDOM $i"; done | sort | sed -r 's/^[0-9]+//' > plabels.1D
 rm labels.1D
 mv plabels.1D labels.1D
 }
@@ -318,7 +320,7 @@ fi
 
 if [ "$permutationmode" = "1" ]; then
     echo "Entering permutation mode"
-    permutation_test 100
+    permutation_test $permcount
 fi
 
 if [ "$totem" = "1" ]; then

From cbdb7eacd26e2de58966d43be261339988627cf3 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 14:55:41 -0500
Subject: [PATCH 22/30] Added matlab code for completing permutation tests

---
 svmbatch/permutation_test.m | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 svmbatch/permutation_test.m

diff --git a/svmbatch/permutation_test.m b/svmbatch/permutation_test.m
new file mode 100644
index 00000000..a44092fc
--- /dev/null
+++ b/svmbatch/permutation_test.m
@@ -0,0 +1,33 @@
+function [Y] = permutation_test(Pt,pdir,name)
+% Calculate nonparametric distributions based on svm permutation tests
+% Pt   - filename of weight vector from real model
+% Pdir - file directory in which to search for results of permutation test
+% img/hdr pairs
+% name - string of name to write out
+
+%% Make list of files
+Pp=spm_select('List',pdir,'[0-9].hdr+')
+
+%% Read in files
+th=spm_vol(Pt);
+ph=spm_vol(Pp);
+
+tvol=spm_read_vols(th);
+pvol=spm_read_vols(ph);
+
+
+%% Create dumping space for comparisons
+
+rvol=zeros(size(tvol));
+rh=th;
+rh.fname=name;
+
+%% Loop over dimensions
+
+for i=1:size(rvol,1), for j=1:size(rvol,2), for k=1:size(rvol,3)
+            rvol(i,j,k)=sum(pvol(i,j,k,:)>tvol(i,j,k))/size(pvol,4);
+        end,end,end
+
+%% Write out the resulting p values
+
+rvol=spm_write_vol(rh,rvol);
\ No newline at end of file

From 21a2e4fd4c8e181b5465834a8f41e0409fa1ffd0 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 14:56:08 -0500
Subject: [PATCH 23/30] Added placeholder for code to rearrange permutation
 tests

---
 svmbatch/perm_test_arrange.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 svmbatch/perm_test_arrange.sh

diff --git a/svmbatch/perm_test_arrange.sh b/svmbatch/perm_test_arrange.sh
new file mode 100644
index 00000000..e69de29b

From 4658ca3da74eb2069fe23a6faca3a45ebb6b49b3 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 15:11:07 -0500
Subject: [PATCH 24/30] updated permutation test results arranged

---
 svmbatch/perm_test_arrange.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/svmbatch/perm_test_arrange.sh b/svmbatch/perm_test_arrange.sh
index e69de29b..845cb31e 100644
--- a/svmbatch/perm_test_arrange.sh
+++ b/svmbatch/perm_test_arrange.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+#A program to reorganize permutation test results from svmbatch for later processing
+
+permdir=  #String pointing to location of the permutation test directories
+
+targetdir= #where you want to put your files after conversion
+
+cd $permdir
+
+weights=`find -name "weight*HEAD"` #get a list of all your weight buckets
+
+let "i=1"
+
+for w in $weights; do
+    3dAFNItoANALYZE -4D $targetdir/$i $w
+    let "i=$i+1"
+done

From 98430460d2642e67c91d942050eb75800e5738da Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Mon, 19 Dec 2011 15:11:23 -0500
Subject: [PATCH 25/30] updated script for permutation test in matlab

---
 svmbatch/permutation_test.m | 1 +
 1 file changed, 1 insertion(+)

diff --git a/svmbatch/permutation_test.m b/svmbatch/permutation_test.m
index a44092fc..fd1b31a9 100644
--- a/svmbatch/permutation_test.m
+++ b/svmbatch/permutation_test.m
@@ -10,6 +10,7 @@
 
 %% Read in files
 th=spm_vol(Pt);
+cd(pdir);
 ph=spm_vol(Pp);
 
 tvol=spm_read_vols(th);

From 35fca2dbe0b18c7597301784a6332db67ad5feb9 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Fri, 6 Jan 2012 13:57:30 -0500
Subject: [PATCH 26/30] Updated supplemental scripts related to permutation
 testing

---
 svmbatch/perm_test_arrange.sh |  6 ++++--
 svmbatch/permutation_test.m   | 20 +++++++++++++++++++-
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/svmbatch/perm_test_arrange.sh b/svmbatch/perm_test_arrange.sh
index 845cb31e..42ce8964 100644
--- a/svmbatch/perm_test_arrange.sh
+++ b/svmbatch/perm_test_arrange.sh
@@ -2,14 +2,16 @@
 
 #A program to reorganize permutation test results from svmbatch for later processing
 
-permdir=  #String pointing to location of the permutation test directories
+permdir='/net/data4/MAS/SVM/FIR_6_10_perms/perms'  #String pointing to location of the permutation test directories
 
-targetdir= #where you want to put your files after conversion
+targetdir='/net/data4/MAS/SVM/FIR_6_10_perms/perms_analyze/' #where you want to put your files after conversion
 
 cd $permdir
 
 weights=`find -name "weight*HEAD"` #get a list of all your weight buckets
 
+mkdir $targetdir
+
 let "i=1"
 
 for w in $weights; do
diff --git a/svmbatch/permutation_test.m b/svmbatch/permutation_test.m
index fd1b31a9..3d915566 100644
--- a/svmbatch/permutation_test.m
+++ b/svmbatch/permutation_test.m
@@ -25,8 +25,26 @@
 
 %% Loop over dimensions
 
+% For each voxel, calculate proportion of permutations that resulted in
+% smaller or equal value. This returns the nonparametric CDF. We then
+% convert this, using norminv, to a z-score. Extremely positive values will
+% have high CDF scores, high p scores, and high z scores. Very negative
+% values will have very small CDF scores, small p scores, and negative z
+% scores. We convert to z for easier visualization in xjview.
+
+for i=1:size(rvol,1), for j=1:size(rvol,2), for k=1:size(rvol,3)
+            rvol(i,j,k)=norminv(sum(pvol(i,j,k,:)<=tvol(i,j,k))/size(pvol,4));
+        end,end,end
+
+%% Mask based on tvol
+% Some voxels that were zero in the real weight vector are out-of-brain
+% voxels. Implicit masking during first level testing should have set them
+% to 0. All permutation tests will likely also return 0, yielding a bizarre
+% value for the CDF. To protect against this, we set the z-score of these
+% points to be 0, for a corresponding p of .5
+
 for i=1:size(rvol,1), for j=1:size(rvol,2), for k=1:size(rvol,3)
-            rvol(i,j,k)=sum(pvol(i,j,k,:)>tvol(i,j,k))/size(pvol,4);
+            if tvol(i,j,k)==0, rvol(i,j,k)=0; end
         end,end,end
 
 %% Write out the resulting p values

From 289566232f0e1c0322768f7e9943ac00875d42dc Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 15 Feb 2012 14:21:52 -0500
Subject: [PATCH 27/30] Some hacky edits of permutation visualization functions

---
 svmbatch/perm_test_arrange.sh | 23 +++++++++++++++---
 svmbatch/permutation_test.m   | 45 +++++++++++++++++++++++++++--------
 2 files changed, 55 insertions(+), 13 deletions(-)
 mode change 100644 => 100755 svmbatch/perm_test_arrange.sh

diff --git a/svmbatch/perm_test_arrange.sh b/svmbatch/perm_test_arrange.sh
old mode 100644
new mode 100755
index 42ce8964..27840b4a
--- a/svmbatch/perm_test_arrange.sh
+++ b/svmbatch/perm_test_arrange.sh
@@ -2,9 +2,25 @@
 
 #A program to reorganize permutation test results from svmbatch for later processing
 
-permdir='/net/data4/MAS/SVM/FIR_6_10_perms/perms'  #String pointing to location of the permutation test directories
 
-targetdir='/net/data4/MAS/SVM/FIR_6_10_perms/perms_analyze/' #where you want to put your files after conversion
+#Parameter Processing
+
+while [ "$1" != "" ]; do
+    case $1 in
+	-p)
+	    shift
+	    permdir=$1
+	    
+	    ;;
+	-t)
+	    shift
+	    targetdir=$1
+	    ;;
+	*)
+	    
+    esac
+    shift
+done
 
 cd $permdir
 
@@ -15,6 +31,7 @@ mkdir $targetdir
 let "i=1"
 
 for w in $weights; do
-    3dAFNItoANALYZE -4D $targetdir/$i $w
+    3dAFNItoANALYZE -4D $targetdir/$i $w >/dev/null
+    echo "Converting file $i"
     let "i=$i+1"
 done
diff --git a/svmbatch/permutation_test.m b/svmbatch/permutation_test.m
index 3d915566..9a41cd5d 100644
--- a/svmbatch/permutation_test.m
+++ b/svmbatch/permutation_test.m
@@ -1,27 +1,29 @@
-function [Y] = permutation_test(Pt,pdir,name)
+%function [Y] = permutation_test(Pt,Pdir,name)
 % Calculate nonparametric distributions based on svm permutation tests
 % Pt   - filename of weight vector from real model
 % Pdir - file directory in which to search for results of permutation test
 % img/hdr pairs
-% name - string of name to write out
+% name - string of name to write out (without .img extension)
 
 %% Make list of files
-Pp=spm_select('List',pdir,'[0-9].hdr+')
+Pp=spm_select('List',Pdir,'[0-9]+\.hdr');
 
 %% Read in files
 th=spm_vol(Pt);
-cd(pdir);
-ph=spm_vol(Pp);
-
 tvol=spm_read_vols(th);
-pvol=spm_read_vols(ph);
 
 
+cd(Pdir);
+ph=spm_vol(Pp);
+pvol=spm_read_vols(ph);
+cd ..
+
 %% Create dumping space for comparisons
 
 rvol=zeros(size(tvol));
 rh=th;
-rh.fname=name;
+rh.fname=[name '.img'];
+rh.descrip='SPM{T_[10000000]}';
 
 %% Loop over dimensions
 
@@ -47,6 +49,29 @@
             if tvol(i,j,k)==0, rvol(i,j,k)=0; end
         end,end,end
 
-%% Write out the resulting p values
+%% Replace Inf and -Inf values with prior min and max, respectively
+% rvol(find(rvol==Inf))=max(rvol(~isinf(rvol)));
+% rvol(find(rvol==-Inf))=min(rvol(~isinf(rvol)));
+
+rvol(find(rvol==Inf))=norminv((1-1/size(pvol,4)));
+rvol(find(rvol==-Inf))=norminv((1/size(pvol,4)));
+
+%Fix the origin for 
+
+rh.mat(:,4)=[-81 -115 -53 1];
+
+
+%% Write out the resulting p values in one giant file
+spm_write_vol(rh,rvol);
+
+%%Slice up the file into its sub-totems, and write them out separately from
+%%bottom up
 
-rvol=spm_write_vol(rh,rvol);
\ No newline at end of file
+for i=1:(th.dim(3)/46)
+    cth_range=[1:46] + (i-1)*46;
+    cth=rh;
+    cth.fname=sprintf('%s%s%s%.3d%s',pwd,'/', name ,i,'.img');
+    cth.dim(3)=[46];
+    ctvol=rvol(:,:,cth_range);
+    spm_write_vol(cth,ctvol);
+end
\ No newline at end of file

From 460eb7d24f714cda30ba0cf967d1d68c5b5431e4 Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 7 Mar 2012 11:33:41 -0500
Subject: [PATCH 28/30] cleaned up matlab portion of permutation testing

---
 .../{ => matlab_Scripts}/permutation_test.m   |  0
 svmbatch/perm_test_arrange.sh                 | 37 -------------------
 2 files changed, 37 deletions(-)
 rename svmbatch/{ => matlab_Scripts}/permutation_test.m (100%)
 delete mode 100755 svmbatch/perm_test_arrange.sh

diff --git a/svmbatch/permutation_test.m b/svmbatch/matlab_Scripts/permutation_test.m
similarity index 100%
rename from svmbatch/permutation_test.m
rename to svmbatch/matlab_Scripts/permutation_test.m
diff --git a/svmbatch/perm_test_arrange.sh b/svmbatch/perm_test_arrange.sh
deleted file mode 100755
index 27840b4a..00000000
--- a/svmbatch/perm_test_arrange.sh
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/bash
-
-#A program to reorganize permutation test results from svmbatch for later processing
-
-
-#Parameter Processing
-
-while [ "$1" != "" ]; do
-    case $1 in
-	-p)
-	    shift
-	    permdir=$1
-	    
-	    ;;
-	-t)
-	    shift
-	    targetdir=$1
-	    ;;
-	*)
-	    
-    esac
-    shift
-done
-
-cd $permdir
-
-weights=`find -name "weight*HEAD"` #get a list of all your weight buckets
-
-mkdir $targetdir
-
-let "i=1"
-
-for w in $weights; do
-    3dAFNItoANALYZE -4D $targetdir/$i $w >/dev/null
-    echo "Converting file $i"
-    let "i=$i+1"
-done

From 652c8503d749b6049909af1d95ba5d41ba01986b Mon Sep 17 00:00:00 2001
From: "Daniel A. Kessler" <kesslerd@umich.edu>
Date: Wed, 7 Mar 2012 11:33:53 -0500
Subject: [PATCH 29/30] updated svmbatch.sh with routines for permutation
 testing

---
 svmbatch/svmbatch.sh | 59 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 46 insertions(+), 13 deletions(-)

diff --git a/svmbatch/svmbatch.sh b/svmbatch/svmbatch.sh
index d46ffa5f..40f2afe1 100755
--- a/svmbatch/svmbatch.sh
+++ b/svmbatch/svmbatch.sh
@@ -282,20 +282,53 @@ for file in $biglist; do
 done
 }
 
+function perms_to_analyze { #Will rewrite all of the weight buckets from the permutation tests as img/hdr pairs for easier readier downstream
+
+    cd $svmdir/perms
+
+    weights=`find -name "weight*HEAD"` #get a list of all your weight buckets
+
+    mkdir $svmdir/perms_analyze
+
+    let "i=1"
+
+    for w in $weights; do
+	3dAFNItoANALYZE -4D $svmdir/perms_analyze/$i $w >/dev/null
+	echo "Converting file $i"
+	let "i=$i+1"
+    done
+
+}
+
+function perms_vizi {
+m64 -nodesktop -nojvm <<EOF
+    Pt = '$svmdir/weightbucket+orig.img'
+    Pdir = '$svmdir/perms_analyze'
+    name= 'permvizi'
+    addpath $thisdir
+    permutation_test.m
+EOF
+
+}
+
+
 function permutation_test { #will perfrom $1 permutations on data, writing out weight buckets at each step
-permute=1
-mkdir $svmdir/perms
-for i in `seq 1 $1`; do
-echo "Running permutation $i of $1"
-svmdir=`echo $svmdir_orig/perms/$i`
-mkdir $svmdir
-cd $svmdir
-ln -s $svmdir_orig/bucketshorttime* .
-cp $svmdir_orig/labels.1D ./labels.1D
-label_permute labels.1D
-set_train_rules
-svm_train "bucketshorttime"
-done
+    permute=1
+    mkdir $svmdir/perms
+    for i in `seq 1 $1`; do
+	echo "Running permutation $i of $1"
+	svmdir=`echo $svmdir_orig/perms/$i`
+	mkdir $svmdir
+	cd $svmdir
+	ln -s $svmdir_orig/bucketshorttime* .
+	cp $svmdir_orig/labels.1D ./labels.1D
+	label_permute labels.1D
+	set_train_rules
+	svm_train "bucketshorttime"
+    done
+perms_to_analyze #Convert all the permutations to image header pairs
+perms_vizi
+    
 }
 
 

From 591fc3afd520993d15e4a89da5dcb9c1bce3473e Mon Sep 17 00:00:00 2001
From: Daniel A Kessler <kesslerd@umich.edu>
Date: Wed, 7 Mar 2012 12:04:53 -0500
Subject: [PATCH 30/30] This empty commit should close #18 by adding the
 current body of svmbatch work into the MethodsCore repo. It should not be
 viewed as the "final" svmbatch product