added phantomas datasets + masks

samuelstjean · Mar 23, 2016 · 7a6a92f · 7a6a92f
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diff --git a/README.md b/README.md
@@ -1,2 +1,17 @@
-# nlsam_data
-Datasets used in the NLSAM paper
+# nlsam datasets repository
+
+Synthetic datasets used in the NLSAM paper, for which the main repo can be found [here](https://github.com/samuelstjean/nlsam/).
+The phantom is based on an earlier version of [phantomas](https://github.com/ecaruyer/phantomas)
+The masks folders contains everything needed for running a tractometer comparison in the proper folders.
+
+The phantomas b1000 and phantomas b3000 folders contains the raw datasets that were used. The naming convention goes as follow
+
++ hardi-scheme contains the bvals/bvecs used by the phantom, which is the same 64 gradient directions for both diffusion weighting.
++ dwis.nii.gz is the noiseless ground-truth data to which noise was added afterward.
++ SNR-(10,15,20 or 30) is the SNR of the dataset computed as SNR = mean(b0) / sigma, with mean(b0) computed inside white matter (see mask) and sigma the noise standard deviation.
++ coils-(1,4,8 or 12) defines the noise distribution as outlined in Eq. 6 of the paper.
++ var-3 means that this dataset has a varying noise profile, which is SNR at the edges and SNR/3 near the center in a linear scale.
+
+Note that not all datasets were used in the original paper, but are still provided here for interested users.
+
+If you would like access to the in-vivo diffusion scan, feel free to contact me.
diff --git a/invivo/encoding_1_2.bval b/invivo/encoding_1_2.bval
diff --git a/invivo/encoding_1_2.bvec b/invivo/encoding_1_2.bvec
diff --git a/masks/bundles/fiber_00.nii b/masks/bundles/fiber_00.nii
diff --git a/masks/bundles/fiber_01.nii b/masks/bundles/fiber_01.nii
diff --git a/masks/bundles/fiber_02.nii b/masks/bundles/fiber_02.nii
diff --git a/masks/bundles/fiber_03.nii b/masks/bundles/fiber_03.nii
diff --git a/masks/bundles/fiber_04.nii b/masks/bundles/fiber_04.nii
diff --git a/masks/bundles/fiber_05.nii b/masks/bundles/fiber_05.nii
diff --git a/masks/bundles/fiber_06.nii b/masks/bundles/fiber_06.nii
diff --git a/masks/bundles/fiber_07.nii b/masks/bundles/fiber_07.nii
diff --git a/masks/bundles/fiber_08.nii b/masks/bundles/fiber_08.nii
diff --git a/masks/bundles/fiber_09.nii b/masks/bundles/fiber_09.nii
diff --git a/masks/bundles/fiber_10.nii b/masks/bundles/fiber_10.nii
diff --git a/masks/bundles/fiber_11.nii b/masks/bundles/fiber_11.nii
diff --git a/masks/bundles/fiber_12.nii b/masks/bundles/fiber_12.nii
diff --git a/masks/bundles/fiber_13.nii b/masks/bundles/fiber_13.nii
diff --git a/masks/bundles/fiber_14.nii b/masks/bundles/fiber_14.nii
diff --git a/masks/bundles/fiber_15.nii b/masks/bundles/fiber_15.nii
diff --git a/masks/bundles/fiber_16.nii b/masks/bundles/fiber_16.nii
diff --git a/masks/bundles/fiber_17.nii b/masks/bundles/fiber_17.nii
diff --git a/masks/bundles/fiber_18.nii b/masks/bundles/fiber_18.nii
diff --git a/masks/bundles/fiber_19.nii b/masks/bundles/fiber_19.nii
diff --git a/masks/bundles/fiber_20.nii b/masks/bundles/fiber_20.nii
diff --git a/masks/bundles/fiber_21.nii b/masks/bundles/fiber_21.nii
diff --git a/masks/bundles/fiber_22.nii b/masks/bundles/fiber_22.nii
diff --git a/masks/bundles/fiber_23.nii b/masks/bundles/fiber_23.nii
diff --git a/masks/bundles/fiber_24.nii b/masks/bundles/fiber_24.nii
diff --git a/masks/bundles/fiber_25.nii b/masks/bundles/fiber_25.nii
diff --git a/masks/bundles/fiber_26.nii b/masks/bundles/fiber_26.nii
diff --git a/masks/mask.nii.gz b/masks/mask.nii.gz
diff --git a/masks/rois.nii.gz b/masks/rois.nii.gz
diff --git a/masks/rois/00_head.nii b/masks/rois/00_head.nii
diff --git a/masks/rois/00_tail.nii b/masks/rois/00_tail.nii
diff --git a/masks/rois/01_head.nii b/masks/rois/01_head.nii
diff --git a/masks/rois/01_tail.nii b/masks/rois/01_tail.nii
diff --git a/masks/rois/02_head.nii b/masks/rois/02_head.nii
diff --git a/masks/rois/02_tail.nii b/masks/rois/02_tail.nii
diff --git a/masks/rois/03_head.nii b/masks/rois/03_head.nii
diff --git a/masks/rois/03_tail.nii b/masks/rois/03_tail.nii
diff --git a/masks/rois/04_head.nii b/masks/rois/04_head.nii
diff --git a/masks/rois/04_tail.nii b/masks/rois/04_tail.nii
diff --git a/masks/rois/05_head.nii b/masks/rois/05_head.nii
diff --git a/masks/rois/05_tail.nii b/masks/rois/05_tail.nii
diff --git a/masks/rois/06_head.nii b/masks/rois/06_head.nii
diff --git a/masks/rois/06_tail.nii b/masks/rois/06_tail.nii
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diff --git a/masks/rois/09_head.nii b/masks/rois/09_head.nii
diff --git a/masks/rois/09_tail.nii b/masks/rois/09_tail.nii
diff --git a/masks/rois/10_head.nii b/masks/rois/10_head.nii
diff --git a/masks/rois/10_tail.nii b/masks/rois/10_tail.nii
diff --git a/masks/rois/11_head.nii b/masks/rois/11_head.nii
diff --git a/masks/rois/11_tail.nii b/masks/rois/11_tail.nii
diff --git a/masks/rois/12_head.nii b/masks/rois/12_head.nii
diff --git a/masks/rois/12_tail.nii b/masks/rois/12_tail.nii
diff --git a/masks/rois/13_head.nii b/masks/rois/13_head.nii
diff --git a/masks/rois/13_tail.nii b/masks/rois/13_tail.nii
diff --git a/masks/rois/14_head.nii b/masks/rois/14_head.nii
diff --git a/masks/rois/14_tail.nii b/masks/rois/14_tail.nii
diff --git a/masks/rois/15_head.nii b/masks/rois/15_head.nii
diff --git a/masks/rois/15_tail.nii b/masks/rois/15_tail.nii
diff --git a/masks/rois/16_head.nii b/masks/rois/16_head.nii
diff --git a/masks/rois/16_tail.nii b/masks/rois/16_tail.nii
diff --git a/masks/rois/17_head.nii b/masks/rois/17_head.nii
diff --git a/masks/rois/17_tail.nii b/masks/rois/17_tail.nii
diff --git a/masks/rois/18_head.nii b/masks/rois/18_head.nii
diff --git a/masks/rois/18_tail.nii b/masks/rois/18_tail.nii
diff --git a/masks/rois/19_head.nii b/masks/rois/19_head.nii
diff --git a/masks/rois/19_tail.nii b/masks/rois/19_tail.nii
diff --git a/masks/rois/20_head.nii b/masks/rois/20_head.nii
diff --git a/masks/rois/20_tail.nii b/masks/rois/20_tail.nii
diff --git a/masks/rois/21_head.nii b/masks/rois/21_head.nii
diff --git a/masks/rois/21_tail.nii b/masks/rois/21_tail.nii
diff --git a/masks/rois/22_head.nii b/masks/rois/22_head.nii
diff --git a/masks/rois/22_tail.nii b/masks/rois/22_tail.nii
diff --git a/masks/rois/23_head.nii b/masks/rois/23_head.nii
diff --git a/masks/rois/23_tail.nii b/masks/rois/23_tail.nii
diff --git a/masks/rois/24_head.nii b/masks/rois/24_head.nii
diff --git a/masks/rois/24_tail.nii b/masks/rois/24_tail.nii
diff --git a/masks/rois/25_head.nii b/masks/rois/25_head.nii
diff --git a/masks/rois/25_tail.nii b/masks/rois/25_tail.nii
diff --git a/masks/rois/26_head.nii b/masks/rois/26_head.nii
diff --git a/masks/rois/26_tail.nii b/masks/rois/26_tail.nii
diff --git a/masks/wm.nii.gz b/masks/wm.nii.gz
diff --git a/phantomas_b1000/dwis.nii.gz b/phantomas_b1000/dwis.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-10_coils-1.nii.gz b/phantomas_b1000/dwis_SNR-10_coils-1.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-10_coils-12.nii.gz b/phantomas_b1000/dwis_SNR-10_coils-12.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-10_coils-12_var-3.nii.gz b/phantomas_b1000/dwis_SNR-10_coils-12_var-3.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-10_coils-1_var-3.nii.gz b/phantomas_b1000/dwis_SNR-10_coils-1_var-3.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-10_coils-4.nii.gz b/phantomas_b1000/dwis_SNR-10_coils-4.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-10_coils-8.nii.gz b/phantomas_b1000/dwis_SNR-10_coils-8.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-15_coils-12_var-3.nii.gz b/phantomas_b1000/dwis_SNR-15_coils-12_var-3.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-15_coils-1_var-3.nii.gz b/phantomas_b1000/dwis_SNR-15_coils-1_var-3.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-20_coils-1.nii.gz b/phantomas_b1000/dwis_SNR-20_coils-1.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-20_coils-12.nii.gz b/phantomas_b1000/dwis_SNR-20_coils-12.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-20_coils-12_var-3.nii.gz b/phantomas_b1000/dwis_SNR-20_coils-12_var-3.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-20_coils-1_var-3.nii.gz b/phantomas_b1000/dwis_SNR-20_coils-1_var-3.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-20_coils-4.nii.gz b/phantomas_b1000/dwis_SNR-20_coils-4.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-20_coils-8.nii.gz b/phantomas_b1000/dwis_SNR-20_coils-8.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-30_coils-1.nii.gz b/phantomas_b1000/dwis_SNR-30_coils-1.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-30_coils-12.nii.gz b/phantomas_b1000/dwis_SNR-30_coils-12.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-30_coils-4.nii.gz b/phantomas_b1000/dwis_SNR-30_coils-4.nii.gz
diff --git a/phantomas_b1000/dwis_SNR-30_coils-8.nii.gz b/phantomas_b1000/dwis_SNR-30_coils-8.nii.gz
diff --git a/phantomas_b1000/hardi-scheme.b b/phantomas_b1000/hardi-scheme.b
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diff --git a/phantomas_b1000/hardi-scheme.bval b/phantomas_b1000/hardi-scheme.bval
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diff --git a/phantomas_b1000/hardi-scheme.bvec b/phantomas_b1000/hardi-scheme.bvec
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diff --git a/phantomas_b3000/dwis.nii.gz b/phantomas_b3000/dwis.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-10_coils-1.nii.gz b/phantomas_b3000/dwis_SNR-10_coils-1.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-10_coils-12.nii.gz b/phantomas_b3000/dwis_SNR-10_coils-12.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-10_coils-12_var-3.nii.gz b/phantomas_b3000/dwis_SNR-10_coils-12_var-3.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-10_coils-1_var-3.nii.gz b/phantomas_b3000/dwis_SNR-10_coils-1_var-3.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-10_coils-4.nii.gz b/phantomas_b3000/dwis_SNR-10_coils-4.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-10_coils-8.nii.gz b/phantomas_b3000/dwis_SNR-10_coils-8.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-15_coils-12_var-3.nii.gz b/phantomas_b3000/dwis_SNR-15_coils-12_var-3.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-15_coils-1_var-3.nii.gz b/phantomas_b3000/dwis_SNR-15_coils-1_var-3.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-20_coils-1.nii.gz b/phantomas_b3000/dwis_SNR-20_coils-1.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-20_coils-12.nii.gz b/phantomas_b3000/dwis_SNR-20_coils-12.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-20_coils-12_var-3.nii.gz b/phantomas_b3000/dwis_SNR-20_coils-12_var-3.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-20_coils-1_var-3.nii.gz b/phantomas_b3000/dwis_SNR-20_coils-1_var-3.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-20_coils-4.nii.gz b/phantomas_b3000/dwis_SNR-20_coils-4.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-20_coils-8.nii.gz b/phantomas_b3000/dwis_SNR-20_coils-8.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-30_coils-1.nii.gz b/phantomas_b3000/dwis_SNR-30_coils-1.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-30_coils-12.nii.gz b/phantomas_b3000/dwis_SNR-30_coils-12.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-30_coils-4.nii.gz b/phantomas_b3000/dwis_SNR-30_coils-4.nii.gz
diff --git a/phantomas_b3000/dwis_SNR-30_coils-8.nii.gz b/phantomas_b3000/dwis_SNR-30_coils-8.nii.gz
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