7T audio-only movie aligned with 3T image space

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "raw/tnt"]
 	path = src/tnt
 	url = ../tnt
+[submodule "src/phase1"]
+	path = src/phase1
+	url = ../phase1

code/aomovie2bold3Tp2.submit

@@ -0,0 +1,238 @@
+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/aligned
+getenv = True
+request_cpus = 1
+request_memory = 4000
+should_transfer_files = NO
+transfer_executable = False
+executable = code/reslice_7to3
+
+#src/phase1/sub-01/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat test.nii.gz
+
+arguments = "src/phase1/sub-01/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-01/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-01/bold7Tp1/brain.nii.gz src/tnt/sub-01/bold3Tp2/brain.nii.gz src/tnt/sub-01/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-01/in_bold3Tp2/sub-01_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-02/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-02/bold7Tp1/brain.nii.gz src/tnt/sub-02/bold3Tp2/brain.nii.gz src/tnt/sub-02/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-02/in_bold3Tp2/sub-02_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-03/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-03/bold7Tp1/brain.nii.gz src/tnt/sub-03/bold3Tp2/brain.nii.gz src/tnt/sub-03/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-03/in_bold3Tp2/sub-03_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-04/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-04/bold7Tp1/brain.nii.gz src/tnt/sub-04/bold3Tp2/brain.nii.gz src/tnt/sub-04/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-04/in_bold3Tp2/sub-04_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-05/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-05/bold7Tp1/brain.nii.gz src/tnt/sub-05/bold3Tp2/brain.nii.gz src/tnt/sub-05/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-05/in_bold3Tp2/sub-05_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-06/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-06/bold7Tp1/brain.nii.gz src/tnt/sub-06/bold3Tp2/brain.nii.gz src/tnt/sub-06/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-06/in_bold3Tp2/sub-06_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-09/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-09/bold7Tp1/brain.nii.gz src/tnt/sub-09/bold3Tp2/brain.nii.gz src/tnt/sub-09/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-09/in_bold3Tp2/sub-09_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-14/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-14/bold7Tp1/brain.nii.gz src/tnt/sub-14/bold3Tp2/brain.nii.gz src/tnt/sub-14/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-14/in_bold3Tp2/sub-14_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-15/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-15/bold7Tp1/brain.nii.gz src/tnt/sub-15/bold3Tp2/brain.nii.gz src/tnt/sub-15/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-15/in_bold3Tp2/sub-15_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-16/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-16/bold7Tp1/brain.nii.gz src/tnt/sub-16/bold3Tp2/brain.nii.gz src/tnt/sub-16/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-16/in_bold3Tp2/sub-16_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-17/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-17/bold7Tp1/brain.nii.gz src/tnt/sub-17/bold3Tp2/brain.nii.gz src/tnt/sub-17/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-17/in_bold3Tp2/sub-17_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-18/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-18/bold7Tp1/brain.nii.gz src/tnt/sub-18/bold3Tp2/brain.nii.gz src/tnt/sub-18/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-18/in_bold3Tp2/sub-18_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-19/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-19/bold7Tp1/brain.nii.gz src/tnt/sub-19/bold3Tp2/brain.nii.gz src/tnt/sub-19/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-19/in_bold3Tp2/sub-19_task-aomovie_run-8_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run001/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-1_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run002/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-2_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run003/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-3_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run004/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-4_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run005/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-5_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run006/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-6_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run007/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-7_bold.nii.gz"
+queue
+arguments = "src/phase1/sub-20/BOLD/task001_run008/bold_dico.nii.gz src/tnt/sub-20/bold7Tp1/brain.nii.gz src/tnt/sub-20/bold3Tp2/brain.nii.gz src/tnt/sub-20/bold7Tp1/in_bold3Tp2/xfm_6dof.mat sub-20/in_bold3Tp2/sub-20_task-aomovie_run-8_bold.nii.gz"
+queue

code/reslice_7to3

@@ -0,0 +1,41 @@
+#!/bin/bash
+# Author: Michael Hanke <michael.hanke@gmail.com>
+# License: MIT
+
+set -e
+set -u
+
+# fake test for FSL
+ignore=$FSLDIR
+
+inbold=$(readlink -f $1) || true
+initref=$(readlink -f $2) || true
+finalref=$(readlink -f $3) || true
+finalxfm=$(readlink -f $4) || true
+outbold=$(readlink -m $5)
+initflirtopts=${6:--dof 6}
+
+for f in "$inbold" "$initref" "$finalref" "$finalxfm"; do
+    if [ -z "$f" ]; then
+      echo "File not found '$1'"
+      exit 1
+    fi
+done
+
+outbolddir=$(dirname "${outbold}")
+mkdir -p "$outbolddir"
+
+wdir=$(mktemp -d --suffix=7to3reslice)
+echo $wdir
+trap "rm -rf $wdir" SIGINT SIGTERM
+cd "$wdir"
+
+$FSLDIR/bin/fslroi "$inbold" bold 0 1
+$FSLDIR/bin/bet bold bold_brain -Z -f 0.1
+$FSLDIR/bin/flirt ${initflirtopts} -in bold_brain -ref $initref -omat bold2brain.mat
+$FSLDIR/bin/convert_xfm -omat bold2final.mat -concat "$finalxfm" bold2brain.mat
+#$FSLDIR/bin/flirt -in bold_brain -ref "$finalref" -applyxfm -init bold2final.mat -out "$outbold" -interp sinc
+$FSLDIR/bin/flirt -in "$inbold" -ref "$finalref" -applyxfm -init bold2final.mat -out "$outbold" -interp sinc
+
+cd -
+rm -rf "$wdir"

src/phase1

@@ -0,0 +1 @@
+Subproject commit b2b9d3e73712def6600c5980bdc52535ca613169

src/tnt

@@ -1 +1 @@
-Subproject commit 4371a70efb3c1945937ea279b0697526948a6a9b
+Subproject commit 8d46ca5786337e910150f272b9af66f8bb6104a1

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/pj/f0/MD5E-s66788945--a03695c7cdacc5d5296f6693a64bdde5.nii.gz/MD5E-s66788945--a03695c7cdacc5d5296f6693a64bdde5.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/x9/Zv/MD5E-s65250909--c59abab209ab7b2af4fb133deb0b880b.nii.gz/MD5E-s65250909--c59abab209ab7b2af4fb133deb0b880b.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/qK/4x/MD5E-s64744386--c3a9726c654a8f29f0455354cd18642d.nii.gz/MD5E-s64744386--c3a9726c654a8f29f0455354cd18642d.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/jf/mK/MD5E-s72185227--3ce7601221c64abcc7fef7347626bd7f.nii.gz/MD5E-s72185227--3ce7601221c64abcc7fef7347626bd7f.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Z2/PJ/MD5E-s68564805--7cd66f6c35d504eec63792001d3eae40.nii.gz/MD5E-s68564805--7cd66f6c35d504eec63792001d3eae40.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/W3/gv/MD5E-s65081248--a47a2c464692fe41f047f17826605c15.nii.gz/MD5E-s65081248--a47a2c464692fe41f047f17826605c15.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/32/MG/MD5E-s80358724--ffa543aa7f537f3040f94470139a6029.nii.gz/MD5E-s80358724--ffa543aa7f537f3040f94470139a6029.nii.gz

sub-01/in_bold3Tp2/sub-01_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/g1/7x/MD5E-s50142582--4c7edd465586a3f3c4213aef2deb47ca.nii.gz/MD5E-s50142582--4c7edd465586a3f3c4213aef2deb47ca.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/21/jJ/MD5E-s69532745--46f0a3adeeb5045685f3c32fd6c41522.nii.gz/MD5E-s69532745--46f0a3adeeb5045685f3c32fd6c41522.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/QJ/j1/MD5E-s67951072--96bd0b9e05706d7912979707f5053d50.nii.gz/MD5E-s67951072--96bd0b9e05706d7912979707f5053d50.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/2k/kj/MD5E-s67501030--9dbc63687b6d6bc5ea7e40c14b8840cf.nii.gz/MD5E-s67501030--9dbc63687b6d6bc5ea7e40c14b8840cf.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/9W/9z/MD5E-s75179111--98e7b4d5cf46765da7e1f7abfeb61076.nii.gz/MD5E-s75179111--98e7b4d5cf46765da7e1f7abfeb61076.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Q4/2j/MD5E-s71068359--734248d4443205ee65af283509c380c4.nii.gz/MD5E-s71068359--734248d4443205ee65af283509c380c4.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/WK/vF/MD5E-s67583262--99011fd7362a6b5f9b354ed01e21a9d6.nii.gz/MD5E-s67583262--99011fd7362a6b5f9b354ed01e21a9d6.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/59/9P/MD5E-s83549910--0f3b56fd01e846735f0db949c1d73d3c.nii.gz/MD5E-s83549910--0f3b56fd01e846735f0db949c1d73d3c.nii.gz

sub-02/in_bold3Tp2/sub-02_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/jz/p0/MD5E-s52135937--c996fced3191b4f87cd813718f045872.nii.gz/MD5E-s52135937--c996fced3191b4f87cd813718f045872.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/VM/4G/MD5E-s65141876--ab9553a84f170edade476b55c49c50ec.nii.gz/MD5E-s65141876--ab9553a84f170edade476b55c49c50ec.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/FW/Wg/MD5E-s63591130--a71500e20b537f80dd44881dedaf0ed2.nii.gz/MD5E-s63591130--a71500e20b537f80dd44881dedaf0ed2.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Vz/gZ/MD5E-s63106968--4bb853d705bbd70d9d92b48ddb7e7e24.nii.gz/MD5E-s63106968--4bb853d705bbd70d9d92b48ddb7e7e24.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/MK/7m/MD5E-s70293982--2296eae0872563551a359605a634df10.nii.gz/MD5E-s70293982--2296eae0872563551a359605a634df10.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/M8/mq/MD5E-s66084647--0e60e16d643770f41ac23f7feea8df14.nii.gz/MD5E-s66084647--0e60e16d643770f41ac23f7feea8df14.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Qf/zk/MD5E-s62707601--2f2e93722c95fdc3ef3d80a26d6d2ded.nii.gz/MD5E-s62707601--2f2e93722c95fdc3ef3d80a26d6d2ded.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/2X/75/MD5E-s77442587--67a1e5e83c1d5c39d20914d510908db0.nii.gz/MD5E-s77442587--67a1e5e83c1d5c39d20914d510908db0.nii.gz

sub-03/in_bold3Tp2/sub-03_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Q8/6J/MD5E-s48346302--c1e0ff787e8c54ddee481a8b666df3de.nii.gz/MD5E-s48346302--c1e0ff787e8c54ddee481a8b666df3de.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/96/74/MD5E-s67168626--4bdf5179e64aaee80ad24e1efe669073.nii.gz/MD5E-s67168626--4bdf5179e64aaee80ad24e1efe669073.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/XK/45/MD5E-s65597281--fdec73df70ad167a8ace5daf340373e8.nii.gz/MD5E-s65597281--fdec73df70ad167a8ace5daf340373e8.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/jF/mk/MD5E-s65299564--b07269845976fd2cee462cec300cc06a.nii.gz/MD5E-s65299564--b07269845976fd2cee462cec300cc06a.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Gq/6p/MD5E-s72850002--261de8562de7ddf0935957908d8e5321.nii.gz/MD5E-s72850002--261de8562de7ddf0935957908d8e5321.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/0v/26/MD5E-s67330985--89afc64b0b79e96c6089ae5abce4abac.nii.gz/MD5E-s67330985--89afc64b0b79e96c6089ae5abce4abac.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/fm/xG/MD5E-s64048083--54da77108130596caa2026b4f7d619a0.nii.gz/MD5E-s64048083--54da77108130596caa2026b4f7d619a0.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/1K/w5/MD5E-s78990497--dd4c76cf6f0da8a42d9a88ddec7bb62c.nii.gz/MD5E-s78990497--dd4c76cf6f0da8a42d9a88ddec7bb62c.nii.gz

sub-04/in_bold3Tp2/sub-04_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/pF/PK/MD5E-s38382622--74cf73f352454fbd12c700c7d988893d.nii.gz/MD5E-s38382622--74cf73f352454fbd12c700c7d988893d.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/QQ/F2/MD5E-s74347138--7df3fc2ff1aaf92ac479998b9b1e4847.nii.gz/MD5E-s74347138--7df3fc2ff1aaf92ac479998b9b1e4847.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/VK/9v/MD5E-s72794138--defe900f09e546f8c45d0851ba528f6b.nii.gz/MD5E-s72794138--defe900f09e546f8c45d0851ba528f6b.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/pW/87/MD5E-s72423440--9948279451f1718e2889fa787a6f5716.nii.gz/MD5E-s72423440--9948279451f1718e2889fa787a6f5716.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Mv/JV/MD5E-s80698367--8c8fb6640ef112bf8f2b89f234d88681.nii.gz/MD5E-s80698367--8c8fb6640ef112bf8f2b89f234d88681.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/v4/pW/MD5E-s74538341--6083406f71e1c56fb4fc1381d6c9760b.nii.gz/MD5E-s74538341--6083406f71e1c56fb4fc1381d6c9760b.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/0W/fP/MD5E-s70905303--9f8d69749fd5dcc91d93ce345c9ce96e.nii.gz/MD5E-s70905303--9f8d69749fd5dcc91d93ce345c9ce96e.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/VF/xV/MD5E-s87465701--90dd53e3acce3769ac290002f6d16393.nii.gz/MD5E-s87465701--90dd53e3acce3769ac290002f6d16393.nii.gz

sub-05/in_bold3Tp2/sub-05_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Vf/72/MD5E-s54578675--a22a256836bcfa0577d021024735a72c.nii.gz/MD5E-s54578675--a22a256836bcfa0577d021024735a72c.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/x3/3F/MD5E-s77154955--3fbdf9081ace2a72297dc384a887fbdf.nii.gz/MD5E-s77154955--3fbdf9081ace2a72297dc384a887fbdf.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/zW/GQ/MD5E-s75285235--189938f965890ef2bfa69fdccc407a43.nii.gz/MD5E-s75285235--189938f965890ef2bfa69fdccc407a43.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/XK/qk/MD5E-s74848440--57b31fb11dfaf2b7c1e76ad54deed29b.nii.gz/MD5E-s74848440--57b31fb11dfaf2b7c1e76ad54deed29b.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/f4/5x/MD5E-s83368383--4709fcc68f4ad149a8d3a38e76ff8c50.nii.gz/MD5E-s83368383--4709fcc68f4ad149a8d3a38e76ff8c50.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/P6/q9/MD5E-s79458723--69eab00ad8ff02b6738e66b865880e37.nii.gz/MD5E-s79458723--69eab00ad8ff02b6738e66b865880e37.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/v8/Kx/MD5E-s75443726--57d20039f484d2cee8365219088a45d7.nii.gz/MD5E-s75443726--57d20039f484d2cee8365219088a45d7.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/9m/k4/MD5E-s93154330--1ab0da189372ea04abd0c564c67ef1d7.nii.gz/MD5E-s93154330--1ab0da189372ea04abd0c564c67ef1d7.nii.gz

sub-06/in_bold3Tp2/sub-06_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/p8/kw/MD5E-s58078067--8c23096fdf9259113f62b3bf6a252e17.nii.gz/MD5E-s58078067--8c23096fdf9259113f62b3bf6a252e17.nii.gz

sub-09/in_bold3Tp2/sub-09_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Fg/8k/MD5E-s73283605--63e178f65c6d29b09eb64eb976c2ee2d.nii.gz/MD5E-s73283605--63e178f65c6d29b09eb64eb976c2ee2d.nii.gz

sub-09/in_bold3Tp2/sub-09_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/k0/gG/MD5E-s71735051--e183fa1fbab12f73e3b76960f274df22.nii.gz/MD5E-s71735051--e183fa1fbab12f73e3b76960f274df22.nii.gz

sub-09/in_bold3Tp2/sub-09_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
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sub-09/in_bold3Tp2/sub-09_task-aomovie_run-4_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/P5/19/MD5E-s79416696--03f62f4eaac6841d00b4492543ad4080.nii.gz/MD5E-s79416696--03f62f4eaac6841d00b4492543ad4080.nii.gz

sub-09/in_bold3Tp2/sub-09_task-aomovie_run-5_bold.nii.gz

@@ -0,0 +1 @@
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sub-09/in_bold3Tp2/sub-09_task-aomovie_run-6_bold.nii.gz

@@ -0,0 +1 @@
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sub-09/in_bold3Tp2/sub-09_task-aomovie_run-7_bold.nii.gz

@@ -0,0 +1 @@
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sub-09/in_bold3Tp2/sub-09_task-aomovie_run-8_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/WP/v4/MD5E-s55224940--7b4795da9f53faca3fa37ab2c990d742.nii.gz/MD5E-s55224940--7b4795da9f53faca3fa37ab2c990d742.nii.gz

sub-14/in_bold3Tp2/sub-14_task-aomovie_run-1_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/QJ/vx/MD5E-s67022602--a9a1a969506c05f59e16272b5a008eda.nii.gz/MD5E-s67022602--a9a1a969506c05f59e16272b5a008eda.nii.gz

sub-14/in_bold3Tp2/sub-14_task-aomovie_run-2_bold.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/KV/wf/MD5E-s65533071--5c0d2d3bb5a68e6367934118b5f315e0.nii.gz/MD5E-s65533071--5c0d2d3bb5a68e6367934118b5f315e0.nii.gz

sub-14/in_bold3Tp2/sub-14_task-aomovie_run-3_bold.nii.gz

@@ -0,0 +1 @@
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