Add 7T vs 3T BOLD transformations

code/mk_xfm_bold7Tp1_vs_bold3Tp2

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+set -e
+set -u
+
+subj=$1
+
+b7dir="${subj}/bold7Tp1"
+b3dir="${subj}/bold3Tp2"
+
+mkdir -p "${b3dir}/in_bold7Tp1"
+mkdir -p "${b7dir}/in_bold3Tp2"
+
+
+$FSLDIR/bin/flirt -dof 6 \
+	-forcescaling -paddingsize 10 -minsampling 1 -bins 256 \
+	-in ${b7dir}/brain \
+	-ref ${b3dir}/brain \
+	-omat "${b7dir}/in_bold3Tp2/xfm_6dof.mat" \
+	-out "${b7dir}/in_bold3Tp2/brain"
+
+$FSLDIR/bin/convert_xfm \
+	-omat "${b3dir}/in_bold7Tp1/xfm_6dof.mat" \
+	-inverse "${b7dir}/in_bold3Tp2/xfm_6dof.mat"
+
+$FSLDIR/bin/flirt \
+	-in "${b3dir}/brain" \
+	-ref "${b7dir}/brain" \
+	-applyxfm \
+	-init "${b3dir}/in_bold7Tp1/xfm_6dof.mat" \
+	-out "${b3dir}/in_bold7Tp1/brain"

code/mk_xfm_bold7Tp1_vs_bold3Tp2.submit

@@ -0,0 +1,42 @@
+universe = vanilla
+output = condor_logs/$(CLUSTER).$(PROCESS).out
+error = condor_logs/$(CLUSTER).$(PROCESS).err
+log = condor_logs/$(CLUSTER).$(PROCESS).log
+initialdir = /home/data/psyinf/forrest_gump/collection/tnt
+getenv = True
+request_cpus = 1
+request_memory = 2000
+should_transfer_files = NO
+transfer_executable = False
+executable = code/mk_xfm_bold7Tp1_vs_bold3Tp2
+
+arguments = sub-01
+queue
+arguments = sub-02
+queue
+arguments = sub-03
+queue
+arguments = sub-04
+queue
+arguments = sub-05
+queue
+arguments = sub-06
+queue
+arguments = sub-09
+queue
+arguments = sub-10
+queue
+arguments = sub-14
+queue
+arguments = sub-15
+queue
+arguments = sub-16
+queue
+arguments = sub-17
+queue
+arguments = sub-18
+queue
+arguments = sub-19
+queue
+arguments = sub-20
+queue

sub-01/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/21/qv/MD5E-s2167356--c99e21ad893032b1e8762be44faaaf07.nii.gz/MD5E-s2167356--c99e21ad893032b1e8762be44faaaf07.nii.gz

sub-01/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/9k/fG/MD5E-s193--2f2f6d187ee991ef13c121289f08bee1.mat/MD5E-s193--2f2f6d187ee991ef13c121289f08bee1.mat

sub-01/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/ZP/Pg/MD5E-s271715--ef6e8cf78b3f003e6b1dfc87d11fc998.nii.gz/MD5E-s271715--ef6e8cf78b3f003e6b1dfc87d11fc998.nii.gz

sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/F7/W1/MD5E-s196--3e8148ed840763ac97d8df0120ce2e1b.mat/MD5E-s196--3e8148ed840763ac97d8df0120ce2e1b.mat

sub-02/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/WZ/7X/MD5E-s2426706--77e5956526b491a70c692773e49a609f.nii.gz/MD5E-s2426706--77e5956526b491a70c692773e49a609f.nii.gz

sub-02/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/wp/Mv/MD5E-s192--912eec71821405be45fa76a53cdf6892.mat/MD5E-s192--912eec71821405be45fa76a53cdf6892.mat

sub-02/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/F2/0M/MD5E-s300921--8ed1e204db87f6fd1cd29f2492c282c6.nii.gz/MD5E-s300921--8ed1e204db87f6fd1cd29f2492c282c6.nii.gz

sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/74/gP/MD5E-s195--9cda0d18daa71810e12f69c94aec7fe0.mat/MD5E-s195--9cda0d18daa71810e12f69c94aec7fe0.mat

sub-03/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/xK/10/MD5E-s1963217--a7ecc2c629980350cb545413c096f231.nii.gz/MD5E-s1963217--a7ecc2c629980350cb545413c096f231.nii.gz

sub-03/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/vw/mP/MD5E-s190--6bf1dbeea8b377fb4cfc844b385100dd.mat/MD5E-s190--6bf1dbeea8b377fb4cfc844b385100dd.mat

sub-03/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/G0/2x/MD5E-s243686--49c998052ea6adcb5236494b80447792.nii.gz/MD5E-s243686--49c998052ea6adcb5236494b80447792.nii.gz

sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/1g/k3/MD5E-s191--f09891a2a3b1f1d4a6ab5347f4c2e3d2.mat/MD5E-s191--f09891a2a3b1f1d4a6ab5347f4c2e3d2.mat

sub-04/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/22/jW/MD5E-s2081351--abfea59f6df18d266ea0d50b9a437abe.nii.gz/MD5E-s2081351--abfea59f6df18d266ea0d50b9a437abe.nii.gz

sub-04/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/Qk/5M/MD5E-s191--0f5921a362a38eeae1b0801b15020014.mat/MD5E-s191--0f5921a362a38eeae1b0801b15020014.mat

sub-04/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/3Z/3m/MD5E-s267202--26764b5d982b03088f7e8ad356dd29d7.nii.gz/MD5E-s267202--26764b5d982b03088f7e8ad356dd29d7.nii.gz

sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/m7/Z9/MD5E-s192--05fbe6544d44db56b5b4651997a9842c.mat/MD5E-s192--05fbe6544d44db56b5b4651997a9842c.mat

sub-05/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/VQ/7P/MD5E-s2001059--40975d9732b0e1b1b7b6b5369824ce0d.nii.gz/MD5E-s2001059--40975d9732b0e1b1b7b6b5369824ce0d.nii.gz

sub-05/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/VM/pk/MD5E-s189--12c6ee3c85604143bef00bc8c81a5a3c.mat/MD5E-s189--12c6ee3c85604143bef00bc8c81a5a3c.mat

sub-05/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/qj/mk/MD5E-s257914--fdefe896104e30245ad3f8c675113932.nii.gz/MD5E-s257914--fdefe896104e30245ad3f8c675113932.nii.gz

sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/K3/pz/MD5E-s194--7125a17a5ef954ceef9edd26c50af15d.mat/MD5E-s194--7125a17a5ef954ceef9edd26c50af15d.mat

sub-06/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/G8/Jf/MD5E-s2426366--e21af31a3b33572aab101c280300d1ca.nii.gz/MD5E-s2426366--e21af31a3b33572aab101c280300d1ca.nii.gz

sub-06/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/Pp/QM/MD5E-s194--093bbd9311a556c67ab8ccd6181c2f2e.mat/MD5E-s194--093bbd9311a556c67ab8ccd6181c2f2e.mat

sub-06/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/64/4J/MD5E-s309639--c59e5b324df4f6b2d4c93d00af8495da.nii.gz/MD5E-s309639--c59e5b324df4f6b2d4c93d00af8495da.nii.gz

sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/qq/gw/MD5E-s196--00ab69d9098cd5e39d1df7fee0f0fcda.mat/MD5E-s196--00ab69d9098cd5e39d1df7fee0f0fcda.mat

sub-09/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/J8/81/MD5E-s2061511--083a1948310b277345a473def760ec2f.nii.gz/MD5E-s2061511--083a1948310b277345a473def760ec2f.nii.gz

sub-09/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/QJ/qv/MD5E-s189--2d7f40d2ee15ab00f5f32fce89fc01e1.mat/MD5E-s189--2d7f40d2ee15ab00f5f32fce89fc01e1.mat

sub-09/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/fW/p8/MD5E-s262147--90288d0571a376f7ea2f04a0d9598845.nii.gz/MD5E-s262147--90288d0571a376f7ea2f04a0d9598845.nii.gz

sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/g0/qM/MD5E-s194--82add439ba8f0ce9c9d8ded09d2ce811.mat/MD5E-s194--82add439ba8f0ce9c9d8ded09d2ce811.mat

sub-10/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/5X/14/MD5E-s1791248--2a267bcc7719505f581b974a9f9701c7.nii.gz/MD5E-s1791248--2a267bcc7719505f581b974a9f9701c7.nii.gz

sub-10/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/p8/gp/MD5E-s193--769ca7e6149ae1cbff42baf0ceb1494c.mat/MD5E-s193--769ca7e6149ae1cbff42baf0ceb1494c.mat

sub-10/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/g4/w7/MD5E-s222639--b4c8481c83c0c4e57f070bc9fd02ddb2.nii.gz/MD5E-s222639--b4c8481c83c0c4e57f070bc9fd02ddb2.nii.gz

sub-10/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/Xk/Kx/MD5E-s193--4a0f92ba30e8d269ee04c3f02eb6c836.mat/MD5E-s193--4a0f92ba30e8d269ee04c3f02eb6c836.mat

sub-14/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/60/6G/MD5E-s1922610--3e1a680984a616b475d979f31c30652c.nii.gz/MD5E-s1922610--3e1a680984a616b475d979f31c30652c.nii.gz

sub-14/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/k5/k9/MD5E-s189--2c3ad2a690d696329713216e13a4c43e.mat/MD5E-s189--2c3ad2a690d696329713216e13a4c43e.mat

sub-14/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/q5/gg/MD5E-s241317--3c51e0f7f2745a7642ef99d686ca61d8.nii.gz/MD5E-s241317--3c51e0f7f2745a7642ef99d686ca61d8.nii.gz

sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/7p/pz/MD5E-s190--b76a30ae7763fed638b24f02bd700422.mat/MD5E-s190--b76a30ae7763fed638b24f02bd700422.mat

sub-15/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/m7/kG/MD5E-s2113726--9ebab280d05b0342d6500a6414739c95.nii.gz/MD5E-s2113726--9ebab280d05b0342d6500a6414739c95.nii.gz

sub-15/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/zZ/7Q/MD5E-s193--3a384cd8e3f28d3ea7b0d0ad30ef320f.mat/MD5E-s193--3a384cd8e3f28d3ea7b0d0ad30ef320f.mat

sub-15/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Xx/WG/MD5E-s272778--8cc1d4c835e1c0bfdf8b0f883f3a16e3.nii.gz/MD5E-s272778--8cc1d4c835e1c0bfdf8b0f883f3a16e3.nii.gz

sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/W4/Wg/MD5E-s195--cf623e143921113f281a32d46eca2c32.mat/MD5E-s195--cf623e143921113f281a32d46eca2c32.mat

sub-16/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Zv/FV/MD5E-s2367250--689eab242aa5db99421e5bf17f81396c.nii.gz/MD5E-s2367250--689eab242aa5db99421e5bf17f81396c.nii.gz

sub-16/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/v1/7x/MD5E-s189--5a7510f034d0dba01337e6eda326db73.mat/MD5E-s189--5a7510f034d0dba01337e6eda326db73.mat

sub-16/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/7G/2m/MD5E-s303352--6ab1ddfecedefadf77446e98bc0bef6e.nii.gz/MD5E-s303352--6ab1ddfecedefadf77446e98bc0bef6e.nii.gz

sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/1p/vk/MD5E-s190--81837c1fec678900db37575d32bf158d.mat/MD5E-s190--81837c1fec678900db37575d32bf158d.mat

sub-17/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/wv/km/MD5E-s1948904--52728a6c62f969ac92b041fb0dfe36a7.nii.gz/MD5E-s1948904--52728a6c62f969ac92b041fb0dfe36a7.nii.gz

sub-17/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/2j/j5/MD5E-s191--cb73df78be007169d08e395176fb05b5.mat/MD5E-s191--cb73df78be007169d08e395176fb05b5.mat

sub-17/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Zq/4g/MD5E-s243273--bafd4930c199f37826a89e3c08794d0a.nii.gz/MD5E-s243273--bafd4930c199f37826a89e3c08794d0a.nii.gz

sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/0F/FZ/MD5E-s194--a3a0f2a18f9657cc87e08cc0648d353e.mat/MD5E-s194--a3a0f2a18f9657cc87e08cc0648d353e.mat

sub-18/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Xx/pz/MD5E-s2058708--e639e4f81616e2c296a2c0384db670fe.nii.gz/MD5E-s2058708--e639e4f81616e2c296a2c0384db670fe.nii.gz

sub-18/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/q1/xQ/MD5E-s190--eb1c9d7cc8a3db691e2bb213ffb4cd50.mat/MD5E-s190--eb1c9d7cc8a3db691e2bb213ffb4cd50.mat

sub-18/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/GK/3X/MD5E-s257229--7d074d8bf9e123d7d5ed6d2889b7858d.nii.gz/MD5E-s257229--7d074d8bf9e123d7d5ed6d2889b7858d.nii.gz

sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/Xx/84/MD5E-s192--7e5f96daceee88a91ca6bb7f592cf669.mat/MD5E-s192--7e5f96daceee88a91ca6bb7f592cf669.mat

sub-19/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Zq/Pm/MD5E-s2108568--439ec0bd381e85e9487694ed0e7b046c.nii.gz/MD5E-s2108568--439ec0bd381e85e9487694ed0e7b046c.nii.gz

sub-19/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/WP/1q/MD5E-s192--7547833a9d7040c431cbdbf8efca1717.mat/MD5E-s192--7547833a9d7040c431cbdbf8efca1717.mat

sub-19/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Z6/Vz/MD5E-s263171--96937877c4207117b8a6bcc05ef2d8d8.nii.gz/MD5E-s263171--96937877c4207117b8a6bcc05ef2d8d8.nii.gz

sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/81/F8/MD5E-s195--ef1381ee4e7482552144a754caa37ce2.mat/MD5E-s195--ef1381ee4e7482552144a754caa37ce2.mat

sub-20/bold3Tp2/in_bold7Tp1/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Ff/9g/MD5E-s2057224--3a394a3e70b3985b4b0dd6ff6725edbc.nii.gz/MD5E-s2057224--3a394a3e70b3985b4b0dd6ff6725edbc.nii.gz

sub-20/bold3Tp2/in_bold7Tp1/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/62/82/MD5E-s191--bfc81fb9610bfc3914262e269158002a.mat/MD5E-s191--bfc81fb9610bfc3914262e269158002a.mat

sub-20/bold7Tp1/in_bold3Tp2/brain.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/7v/qv/MD5E-s254944--4c47f516d3cdc6643a405bc2de7c7813.nii.gz/MD5E-s254944--4c47f516d3cdc6643a405bc2de7c7813.nii.gz

sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat

@@ -0,0 +1 @@
+../../../.git/annex/objects/qp/7w/MD5E-s190--b88a37881bfc40a39dbd7abf32187c09.mat/MD5E-s190--b88a37881bfc40a39dbd7abf32187c09.mat