Per scan tSNR image

code/calc_per_3Tscan_tsnr.submit

@@ -0,0 +1,522 @@
+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 = 2000
+should_transfer_files = NO
+transfer_executable = False
+executable = /home/data/psyinf/forrest_gump/collection/aligned/code/calc_tsnr
+
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+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-1_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-2_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-3_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-4_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-5_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-6_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-7_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-avmovie_run-8_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-movielocalizer_run-1_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-objectcategories_run-1_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-objectcategories_run-2_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-objectcategories_run-3_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-objectcategories_run-4_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-retmap_run-1_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-retmap_run-2_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-retmap_run-3_bold.nii.gz
+queue
+arguments = sub-18/in_bold3Tp2/sub-18_task-retmap_run-4_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-1_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-2_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-3_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-4_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-5_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-6_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-7_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-avmovie_run-8_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-movielocalizer_run-1_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-objectcategories_run-1_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-objectcategories_run-2_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-objectcategories_run-3_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-objectcategories_run-4_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-retmap_run-1_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-retmap_run-2_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-retmap_run-3_bold.nii.gz
+queue
+arguments = sub-19/in_bold3Tp2/sub-19_task-retmap_run-4_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-1_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-2_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-3_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-4_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-5_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-6_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-7_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-avmovie_run-8_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-movielocalizer_run-1_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-objectcategories_run-1_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-objectcategories_run-2_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-objectcategories_run-3_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-objectcategories_run-4_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-retmap_run-1_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-retmap_run-2_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-retmap_run-3_bold.nii.gz
+queue
+arguments = sub-20/in_bold3Tp2/sub-20_task-retmap_run-4_bold.nii.gz
+queue

code/calc_tsnr

@@ -0,0 +1,39 @@
+#!/usr/bin/python
+"""
+Compute a tSNR volume given an input time series image.
+"""
+
+import os
+import sys
+
+if not len(sys.argv) == 2:
+    print __doc__
+    sys.exit(1)
+
+import nibabel as nb
+from mvpa2.mappers.detrend import poly_detrend
+from mvpa2.datasets.mri import fmri_dataset
+from mvpa2.datasets.mri import map2nifti
+
+infilename = sys.argv[1]
+outfilename = os.path.splitext(infilename)[0]
+if outfilename.endswith('.nii'):
+    outfilename = os.path.splitext(outfilename)[0]
+outfilename += '_tsnr.nii.gz'
+
+ds = fmri_dataset(infilename)
+# clip the value range, can only be negative due to interpolation
+# regime
+ds.samples[ds.samples < 0] = 0
+# first capture mean -- detrending will bring it close to zero
+m = ds.samples.mean(axis=0)
+# now detrend
+poly_detrend(ds, polyord=1)
+# and get the std after linear trend removal
+std = ds.samples.std(axis=0)
+# compute tSNR
+m[std > 0] /= std[std > 0]
+# protect against ultra-low noise voxels (images are zero'ed at the edges)
+m[m > 1000] = 1000
+
+map2nifti(ds, m).to_filename(outfilename)

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/6G/5k/MD5E-s392748--5641d31871351b37001ea4e74b83d9e6.nii.gz/MD5E-s392748--5641d31871351b37001ea4e74b83d9e6.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-2_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/QM/6J/MD5E-s390389--d97cd7992938109fba2c513a026b29dc.nii.gz/MD5E-s390389--d97cd7992938109fba2c513a026b29dc.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-3_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/kg/25/MD5E-s384080--76a8d94d54201608e8f0efb6a6716bc4.nii.gz/MD5E-s384080--76a8d94d54201608e8f0efb6a6716bc4.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-4_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Qj/5J/MD5E-s381026--c4429b4d82f811d07281d6409d891b49.nii.gz/MD5E-s381026--c4429b4d82f811d07281d6409d891b49.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-5_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/gG/v8/MD5E-s390558--30d384adc6c1039fb8b920cb908fa45c.nii.gz/MD5E-s390558--30d384adc6c1039fb8b920cb908fa45c.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-6_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/k8/Z9/MD5E-s360092--04031bba06eb223de085f6f0958e0776.nii.gz/MD5E-s360092--04031bba06eb223de085f6f0958e0776.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-7_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/m8/qj/MD5E-s391011--1e49dac72bfc3f57084e221fb5b2347a.nii.gz/MD5E-s391011--1e49dac72bfc3f57084e221fb5b2347a.nii.gz

sub-01/in_bold3Tp2/sub-01_task-avmovie_run-8_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/qX/9k/MD5E-s359877--93453423ce0bc58f94511c5bf30c42e1.nii.gz/MD5E-s359877--93453423ce0bc58f94511c5bf30c42e1.nii.gz

sub-01/in_bold3Tp2/sub-01_task-movielocalizer_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/vK/mK/MD5E-s342860--b55e8cec713f70da671444d8a588ca4e.nii.gz/MD5E-s342860--b55e8cec713f70da671444d8a588ca4e.nii.gz

sub-01/in_bold3Tp2/sub-01_task-objectcategories_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/X7/P8/MD5E-s353253--cac72dcac7c1f41219c2322f901637b4.nii.gz/MD5E-s353253--cac72dcac7c1f41219c2322f901637b4.nii.gz

sub-01/in_bold3Tp2/sub-01_task-objectcategories_run-2_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/4M/0V/MD5E-s353401--6b8537eae555b18fd8e07d864345baf6.nii.gz/MD5E-s353401--6b8537eae555b18fd8e07d864345baf6.nii.gz

sub-01/in_bold3Tp2/sub-01_task-objectcategories_run-3_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/jj/GK/MD5E-s352436--0a67ef04d7dc047aa07376cadf897fd4.nii.gz/MD5E-s352436--0a67ef04d7dc047aa07376cadf897fd4.nii.gz

sub-01/in_bold3Tp2/sub-01_task-objectcategories_run-4_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/px/2p/MD5E-s352887--c814949bf1a349d6caceb107c8567f1d.nii.gz/MD5E-s352887--c814949bf1a349d6caceb107c8567f1d.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/gP/67/MD5E-s349621--b43a574dc04d474381036a2cdf143796.nii.gz/MD5E-s349621--b43a574dc04d474381036a2cdf143796.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/8z/0z/MD5E-s349237--bd31fffd4c5ed127da321b16bdf7c914.nii.gz/MD5E-s349237--bd31fffd4c5ed127da321b16bdf7c914.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/G5/q6/MD5E-s351221--54713505df95b8be65cc56ed7b990610.nii.gz/MD5E-s351221--54713505df95b8be65cc56ed7b990610.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/2V/Pk/MD5E-s350710--cdb4bd2e00d6e0ae0a799f2ef4a77d23.nii.gz/MD5E-s350710--cdb4bd2e00d6e0ae0a799f2ef4a77d23.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/5X/GJ/MD5E-s428827--4cad2057567a42ab7af054a90bf029e6.nii.gz/MD5E-s428827--4cad2057567a42ab7af054a90bf029e6.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-2_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/qG/Qm/MD5E-s428729--09da14f6b951ea04b0bf35094d6c8f3a.nii.gz/MD5E-s428729--09da14f6b951ea04b0bf35094d6c8f3a.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-3_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/0F/XQ/MD5E-s390455--909660044b6a3c38afd7407c996104da.nii.gz/MD5E-s390455--909660044b6a3c38afd7407c996104da.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-4_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/ZZ/x3/MD5E-s389217--f22e905286d443506e93f5116c45a52f.nii.gz/MD5E-s389217--f22e905286d443506e93f5116c45a52f.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-5_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/xJ/8f/MD5E-s431731--76d57457988dd4b3af4d288d2dbc0c87.nii.gz/MD5E-s431731--76d57457988dd4b3af4d288d2dbc0c87.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-6_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/36/Jw/MD5E-s432063--d204e1a642aa1c0d9f83439d1ce4152b.nii.gz/MD5E-s432063--d204e1a642aa1c0d9f83439d1ce4152b.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-7_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/0q/z7/MD5E-s431976--2c0bebe08c1a279bac742dea12513a6e.nii.gz/MD5E-s431976--2c0bebe08c1a279bac742dea12513a6e.nii.gz

sub-02/in_bold3Tp2/sub-02_task-avmovie_run-8_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Vv/9Z/MD5E-s390802--f2eb15ed7210b8eb526026dea84ad97b.nii.gz/MD5E-s390802--f2eb15ed7210b8eb526026dea84ad97b.nii.gz

sub-02/in_bold3Tp2/sub-02_task-movielocalizer_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/V9/p1/MD5E-s379346--f2bff3204ca147f3dce60120c6711a58.nii.gz/MD5E-s379346--f2bff3204ca147f3dce60120c6711a58.nii.gz

sub-02/in_bold3Tp2/sub-02_task-objectcategories_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Mp/Mz/MD5E-s386130--3cf090260abfa6ae9d35428d78a67901.nii.gz/MD5E-s386130--3cf090260abfa6ae9d35428d78a67901.nii.gz

sub-02/in_bold3Tp2/sub-02_task-objectcategories_run-2_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/gZ/Kf/MD5E-s385440--dca6fa098bffb5e125e9638e2c28a8d5.nii.gz/MD5E-s385440--dca6fa098bffb5e125e9638e2c28a8d5.nii.gz

sub-02/in_bold3Tp2/sub-02_task-objectcategories_run-3_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/kV/FZ/MD5E-s385178--8e6dac10805286e0bad3949577a7d130.nii.gz/MD5E-s385178--8e6dac10805286e0bad3949577a7d130.nii.gz

sub-02/in_bold3Tp2/sub-02_task-objectcategories_run-4_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/vG/3m/MD5E-s385718--b8f49406b56eea924f51023601831355.nii.gz/MD5E-s385718--b8f49406b56eea924f51023601831355.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/52/Mw/MD5E-s384581--b0f25214e545f35e71509c87e21eb2e5.nii.gz/MD5E-s384581--b0f25214e545f35e71509c87e21eb2e5.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/zm/vZ/MD5E-s383385--c7b2f68614a0f1c103f3e6f74d3cf260.nii.gz/MD5E-s383385--c7b2f68614a0f1c103f3e6f74d3cf260.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/5w/Gv/MD5E-s383960--873380ca6398f6ed38995da0c8dfa9e2.nii.gz/MD5E-s383960--873380ca6398f6ed38995da0c8dfa9e2.nii.gz

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

@@ -0,0 +1 @@
+../../.git/annex/objects/g8/pz/MD5E-s383403--4f3d2751bc006e6b9964c6a7a89180a8.nii.gz/MD5E-s383403--4f3d2751bc006e6b9964c6a7a89180a8.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Z4/Vp/MD5E-s357915--10833e67056420f8718ed84b8dfbe8ca.nii.gz/MD5E-s357915--10833e67056420f8718ed84b8dfbe8ca.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-2_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/65/jf/MD5E-s357778--a25755439450e9a33d46336877dcfb02.nii.gz/MD5E-s357778--a25755439450e9a33d46336877dcfb02.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-3_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/g7/6F/MD5E-s357778--405974698102f3af1c83c7b2f5b9d227.nii.gz/MD5E-s357778--405974698102f3af1c83c7b2f5b9d227.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-4_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/m9/km/MD5E-s360467--d8a34d2500e75473c92c45a6f535870e.nii.gz/MD5E-s360467--d8a34d2500e75473c92c45a6f535870e.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-5_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/V2/96/MD5E-s337408--62f1b84e7cfc47dd033e05f639840a0b.nii.gz/MD5E-s337408--62f1b84e7cfc47dd033e05f639840a0b.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-6_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/zV/KZ/MD5E-s336258--f0217fb916b782d81835ecb24f92541a.nii.gz/MD5E-s336258--f0217fb916b782d81835ecb24f92541a.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-7_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/Zx/46/MD5E-s333792--172d659df8c8f5549d297a45f5e45f3c.nii.gz/MD5E-s333792--172d659df8c8f5549d297a45f5e45f3c.nii.gz

sub-03/in_bold3Tp2/sub-03_task-avmovie_run-8_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/x4/zF/MD5E-s361275--1d6e645b071f1273586d44f0b01de68d.nii.gz/MD5E-s361275--1d6e645b071f1273586d44f0b01de68d.nii.gz

sub-03/in_bold3Tp2/sub-03_task-movielocalizer_run-1_bold_tsnr.nii.gz

@@ -0,0 +1 @@
+../../.git/annex/objects/ZX/pg/MD5E-s345597--7ff6c5c2f0b2dc0421843f9b1dba2b8f.nii.gz/MD5E-s345597--7ff6c5c2f0b2dc0421843f9b1dba2b8f.nii.gz

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