Align retmap data to subject bold3Tp2 template + code

code/retmap_motion_correction.submit

@@ -0,0 +1,132 @@
+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 = /home/data/psyinf/forrest_gump/collection/aligned/code/mcflirt_2stage
+
+arguments = raw/phase2/sub-01/ses-localizer/func/sub-01_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-01/bold3Tp2/brain.nii.gz sub-01/in_bold3Tp2/sub-01_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-01/ses-localizer/func/sub-01_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-01/bold3Tp2/brain.nii.gz sub-01/in_bold3Tp2/sub-01_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-01/ses-localizer/func/sub-01_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-01/bold3Tp2/brain.nii.gz sub-01/in_bold3Tp2/sub-01_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-01/ses-localizer/func/sub-01_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-01/bold3Tp2/brain.nii.gz sub-01/in_bold3Tp2/sub-01_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-02/ses-localizer/func/sub-02_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-02/bold3Tp2/brain.nii.gz sub-02/in_bold3Tp2/sub-02_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-02/ses-localizer/func/sub-02_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-02/bold3Tp2/brain.nii.gz sub-02/in_bold3Tp2/sub-02_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-02/ses-localizer/func/sub-02_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-02/bold3Tp2/brain.nii.gz sub-02/in_bold3Tp2/sub-02_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-02/ses-localizer/func/sub-02_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-02/bold3Tp2/brain.nii.gz sub-02/in_bold3Tp2/sub-02_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-03/ses-localizer/func/sub-03_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-03/bold3Tp2/brain.nii.gz sub-03/in_bold3Tp2/sub-03_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-03/ses-localizer/func/sub-03_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-03/bold3Tp2/brain.nii.gz sub-03/in_bold3Tp2/sub-03_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-03/ses-localizer/func/sub-03_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-03/bold3Tp2/brain.nii.gz sub-03/in_bold3Tp2/sub-03_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-03/ses-localizer/func/sub-03_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-03/bold3Tp2/brain.nii.gz sub-03/in_bold3Tp2/sub-03_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-04/ses-localizer/func/sub-04_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-04/bold3Tp2/brain.nii.gz sub-04/in_bold3Tp2/sub-04_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-04/ses-localizer/func/sub-04_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-04/bold3Tp2/brain.nii.gz sub-04/in_bold3Tp2/sub-04_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-04/ses-localizer/func/sub-04_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-04/bold3Tp2/brain.nii.gz sub-04/in_bold3Tp2/sub-04_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-04/ses-localizer/func/sub-04_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-04/bold3Tp2/brain.nii.gz sub-04/in_bold3Tp2/sub-04_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-05/ses-localizer/func/sub-05_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-05/bold3Tp2/brain.nii.gz sub-05/in_bold3Tp2/sub-05_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-05/ses-localizer/func/sub-05_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-05/bold3Tp2/brain.nii.gz sub-05/in_bold3Tp2/sub-05_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-05/ses-localizer/func/sub-05_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-05/bold3Tp2/brain.nii.gz sub-05/in_bold3Tp2/sub-05_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-05/ses-localizer/func/sub-05_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-05/bold3Tp2/brain.nii.gz sub-05/in_bold3Tp2/sub-05_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-06/ses-localizer/func/sub-06_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-06/bold3Tp2/brain.nii.gz sub-06/in_bold3Tp2/sub-06_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-06/ses-localizer/func/sub-06_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-06/bold3Tp2/brain.nii.gz sub-06/in_bold3Tp2/sub-06_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-06/ses-localizer/func/sub-06_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-06/bold3Tp2/brain.nii.gz sub-06/in_bold3Tp2/sub-06_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-06/ses-localizer/func/sub-06_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-06/bold3Tp2/brain.nii.gz sub-06/in_bold3Tp2/sub-06_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-09/ses-localizer/func/sub-09_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-09/bold3Tp2/brain.nii.gz sub-09/in_bold3Tp2/sub-09_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-09/ses-localizer/func/sub-09_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-09/bold3Tp2/brain.nii.gz sub-09/in_bold3Tp2/sub-09_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-09/ses-localizer/func/sub-09_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-09/bold3Tp2/brain.nii.gz sub-09/in_bold3Tp2/sub-09_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-09/ses-localizer/func/sub-09_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-09/bold3Tp2/brain.nii.gz sub-09/in_bold3Tp2/sub-09_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-10/ses-localizer/func/sub-10_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-10/bold3Tp2/brain.nii.gz sub-10/in_bold3Tp2/sub-10_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-10/ses-localizer/func/sub-10_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-10/bold3Tp2/brain.nii.gz sub-10/in_bold3Tp2/sub-10_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-10/ses-localizer/func/sub-10_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-10/bold3Tp2/brain.nii.gz sub-10/in_bold3Tp2/sub-10_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-10/ses-localizer/func/sub-10_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-10/bold3Tp2/brain.nii.gz sub-10/in_bold3Tp2/sub-10_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-14/ses-localizer/func/sub-14_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-14/bold3Tp2/brain.nii.gz sub-14/in_bold3Tp2/sub-14_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-14/ses-localizer/func/sub-14_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-14/bold3Tp2/brain.nii.gz sub-14/in_bold3Tp2/sub-14_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-14/ses-localizer/func/sub-14_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-14/bold3Tp2/brain.nii.gz sub-14/in_bold3Tp2/sub-14_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-14/ses-localizer/func/sub-14_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-14/bold3Tp2/brain.nii.gz sub-14/in_bold3Tp2/sub-14_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-15/ses-localizer/func/sub-15_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-15/bold3Tp2/brain.nii.gz sub-15/in_bold3Tp2/sub-15_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-15/ses-localizer/func/sub-15_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-15/bold3Tp2/brain.nii.gz sub-15/in_bold3Tp2/sub-15_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-15/ses-localizer/func/sub-15_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-15/bold3Tp2/brain.nii.gz sub-15/in_bold3Tp2/sub-15_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-15/ses-localizer/func/sub-15_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-15/bold3Tp2/brain.nii.gz sub-15/in_bold3Tp2/sub-15_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-16/ses-localizer/func/sub-16_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-16/bold3Tp2/brain.nii.gz sub-16/in_bold3Tp2/sub-16_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-16/ses-localizer/func/sub-16_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-16/bold3Tp2/brain.nii.gz sub-16/in_bold3Tp2/sub-16_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-16/ses-localizer/func/sub-16_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-16/bold3Tp2/brain.nii.gz sub-16/in_bold3Tp2/sub-16_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-16/ses-localizer/func/sub-16_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-16/bold3Tp2/brain.nii.gz sub-16/in_bold3Tp2/sub-16_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-17/bold3Tp2/brain.nii.gz sub-17/in_bold3Tp2/sub-17_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-17/bold3Tp2/brain.nii.gz sub-17/in_bold3Tp2/sub-17_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-17/bold3Tp2/brain.nii.gz sub-17/in_bold3Tp2/sub-17_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-17/bold3Tp2/brain.nii.gz sub-17/in_bold3Tp2/sub-17_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-18/ses-localizer/func/sub-18_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-18/bold3Tp2/brain.nii.gz sub-18/in_bold3Tp2/sub-18_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-18/ses-localizer/func/sub-18_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-18/bold3Tp2/brain.nii.gz sub-18/in_bold3Tp2/sub-18_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-18/ses-localizer/func/sub-18_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-18/bold3Tp2/brain.nii.gz sub-18/in_bold3Tp2/sub-18_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-18/ses-localizer/func/sub-18_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-18/bold3Tp2/brain.nii.gz sub-18/in_bold3Tp2/sub-18_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-19/ses-localizer/func/sub-19_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-19/bold3Tp2/brain.nii.gz sub-19/in_bold3Tp2/sub-19_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-19/ses-localizer/func/sub-19_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-19/bold3Tp2/brain.nii.gz sub-19/in_bold3Tp2/sub-19_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-19/ses-localizer/func/sub-19_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-19/bold3Tp2/brain.nii.gz sub-19/in_bold3Tp2/sub-19_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-19/ses-localizer/func/sub-19_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-19/bold3Tp2/brain.nii.gz sub-19/in_bold3Tp2/sub-19_task-retmap_run-4_bold.nii.gz
+queue
+arguments = raw/phase2/sub-20/ses-localizer/func/sub-20_ses-localizer_task-retmap_run-1_bold.nii.gz raw/tnt/sub-20/bold3Tp2/brain.nii.gz sub-20/in_bold3Tp2/sub-20_task-retmap_run-1_bold.nii.gz
+queue
+arguments = raw/phase2/sub-20/ses-localizer/func/sub-20_ses-localizer_task-retmap_run-2_bold.nii.gz raw/tnt/sub-20/bold3Tp2/brain.nii.gz sub-20/in_bold3Tp2/sub-20_task-retmap_run-2_bold.nii.gz
+queue
+arguments = raw/phase2/sub-20/ses-localizer/func/sub-20_ses-localizer_task-retmap_run-3_bold.nii.gz raw/tnt/sub-20/bold3Tp2/brain.nii.gz sub-20/in_bold3Tp2/sub-20_task-retmap_run-3_bold.nii.gz
+queue
+arguments = raw/phase2/sub-20/ses-localizer/func/sub-20_ses-localizer_task-retmap_run-4_bold.nii.gz raw/tnt/sub-20/bold3Tp2/brain.nii.gz sub-20/in_bold3Tp2/sub-20_task-retmap_run-4_bold.nii.gz
+queue

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

@@ -0,0 +1 @@
+../../.git/annex/objects/ZX/62/MD5E-s19410560--084ac9d8c17ac3472a73a096a4f375e7.nii.gz/MD5E-s19410560--084ac9d8c17ac3472a73a096a4f375e7.nii.gz

sub-01/in_bold3Tp2/sub-01_task-retmap_run-1_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/qK/xq/MD5E-s6505--bf37c49764fb276c1e2dc36943ab9d7b.txt/MD5E-s6505--bf37c49764fb276c1e2dc36943ab9d7b.txt

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

@@ -0,0 +1 @@
+../../.git/annex/objects/6f/8j/MD5E-s19456803--169dac350120a68108cdc1c40b2a15bf.nii.gz/MD5E-s19456803--169dac350120a68108cdc1c40b2a15bf.nii.gz

sub-01/in_bold3Tp2/sub-01_task-retmap_run-2_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/vq/w8/MD5E-s6574--125d172e3f6810109e35b549e74d6249.txt/MD5E-s6574--125d172e3f6810109e35b549e74d6249.txt

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

@@ -0,0 +1 @@
+../../.git/annex/objects/7F/vv/MD5E-s19569169--5c9af43d53769f356819b22497d4327b.nii.gz/MD5E-s19569169--5c9af43d53769f356819b22497d4327b.nii.gz

sub-01/in_bold3Tp2/sub-01_task-retmap_run-3_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/G2/GQ/MD5E-s6602--c48ca85072cd9a51878fbb00a7d1a19c.txt/MD5E-s6602--c48ca85072cd9a51878fbb00a7d1a19c.txt

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

@@ -0,0 +1 @@
+../../.git/annex/objects/Vm/k3/MD5E-s19575825--6af80352b476b849a5fa5df060f6f51a.nii.gz/MD5E-s19575825--6af80352b476b849a5fa5df060f6f51a.nii.gz

sub-01/in_bold3Tp2/sub-01_task-retmap_run-4_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/qJ/J7/MD5E-s6574--7cc36c8140a6beadfc33dc90824b7298.txt/MD5E-s6574--7cc36c8140a6beadfc33dc90824b7298.txt

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

@@ -0,0 +1 @@
+../../.git/annex/objects/18/K4/MD5E-s21916904--09b3566b339a4a4411f0835f1a342c0e.nii.gz/MD5E-s21916904--09b3566b339a4a4411f0835f1a342c0e.nii.gz

sub-02/in_bold3Tp2/sub-02_task-retmap_run-1_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/qK/vk/MD5E-s6754--65191488255d19302f645c1878eacb3b.txt/MD5E-s6754--65191488255d19302f645c1878eacb3b.txt

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

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+../../.git/annex/objects/kv/93/MD5E-s21919278--d05e09bd501f1ffe6286531adc65b0c0.nii.gz/MD5E-s21919278--d05e09bd501f1ffe6286531adc65b0c0.nii.gz

sub-02/in_bold3Tp2/sub-02_task-retmap_run-2_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/pq/30/MD5E-s6593--2d4b9b20bf822487561161ea8c606fe3.txt/MD5E-s6593--2d4b9b20bf822487561161ea8c606fe3.txt

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

@@ -0,0 +1 @@
+../../.git/annex/objects/pf/16/MD5E-s21846996--4c0f527e6244b53365c8244a98308ab2.nii.gz/MD5E-s21846996--4c0f527e6244b53365c8244a98308ab2.nii.gz

sub-02/in_bold3Tp2/sub-02_task-retmap_run-3_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/19/4J/MD5E-s6756--62bee797a95644cb82350b7135113915.txt/MD5E-s6756--62bee797a95644cb82350b7135113915.txt

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

@@ -0,0 +1 @@
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sub-02/in_bold3Tp2/sub-02_task-retmap_run-4_bold_mcparams.txt

@@ -0,0 +1 @@
+../../.git/annex/objects/j7/vJ/MD5E-s6687--7a41fc93039b6cbccc69e23e7440defe.txt/MD5E-s6687--7a41fc93039b6cbccc69e23e7440defe.txt

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