diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp index b2a1020..a2db9eb 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp @@ -1,145 +1,145 @@ 0 0.10000000000000001 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true false false true 196 254 11 0.699999988 0.699999988 0.699999988 68.1999969 104.300003 11.999999 -1 0 0 0 -1 0 0 0 1 0 0 1 false 0.75 7828.38916 5520 921 90 1 50 true 0 true false 5 1 0.397000015 - 0.0199999996 + 0.0016 70 1 0.0649999976 false true 5 0 0 0 0 10 random false false false false false false false false false true StickTensorBallBall _RELAX_SPIKES_MOTION /tmp/ fiber stick 0.0020500000000000002 41 402 1 fiber tensor 0.0015 0.00042999999999999999 0.00042999999999999999 63 1764 2 non-fiber ball 0.00064999999999999997 68 1115 3 non-fiber ball 0.0028 885 4582 4 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs index 142a43c..09a4cc9 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs @@ -1,3 +1,3 @@ 0 1 1 1 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 1 1 1 0 0 0 0 0 +0 0 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.nii.gz index 4b65a8a..03e08c8 100644 Binary files a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.nii.gz and b/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp index 835b424..da33ca9 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp @@ -1,145 +1,145 @@ 0 0.10000000000000001 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true false false true 196 254 11 0.699999988 0.699999988 0.699999988 68.1999969 104.300003 11.999999 -1 0 0 0 -1 0 0 0 1 0 0 1 false 0.75 7828.38916 5520 921 90 1 50 true 0 true false 5 1 0.397000015 - 0.0199999996 + 0.0016 70 1 0.0649999976 true true 5 0 0 0 0 10 random false false false false true false false false false true StickTensorBallBall _RELAX_SPIKES_MOTION /tmp/ fiber stick 0.0020500000000000002 41 402 1 fiber tensor 0.0015 0.00042999999999999999 0.00042999999999999999 63 1764 2 non-fiber ball 0.00064999999999999997 68 1115 3 non-fiber ball 0.0028 885 4582 4 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz index dfde5ef..840a846 100644 Binary files a/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz and b/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp index 70fe67c..7e936d0 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp @@ -1,145 +1,145 @@ 0 0.10000000000000001 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true false false true 196 254 11 0.699999988 0.699999988 0.699999988 68.1999969 104.300003 11.999999 -1 0 0 0 -1 0 0 0 1 0 0 1 false 0.75 7828.38916 5520 921 90 1 50 true 0 true false 5 1 0.397000015 - 0.0199999996 + 0.0016 70 1 0.0649999976 false true 5 0 0 0 0 10 random false false false false false false false true false true StickTensorBallBall _RELAX_SPIKES_MOTION /tmp/ fiber stick 0.0020500000000000002 41 402 1 fiber tensor 0.0015 0.00042999999999999999 0.00042999999999999999 63 1764 2 non-fiber ball 0.00064999999999999997 68 1115 3 non-fiber ball 0.0028 885 4582 4 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz index dea5053..fbf2c4d 100644 Binary files a/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz and b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp similarity index 95% copy from DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp copy to DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp index b2a1020..5ecda26 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp @@ -1,145 +1,145 @@ 0 0.10000000000000001 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true false false true 196 254 11 0.699999988 0.699999988 0.699999988 68.1999969 104.300003 11.999999 -1 0 0 0 -1 0 0 0 1 0 0 1 false 0.75 7828.38916 5520 921 90 1 50 true 0 true false 5 1 0.397000015 - 0.0199999996 + 0.0016 70 1 0.0649999976 false true 5 0 0 0 0 10 random false - false - false + true + true false false - false + true false false false true StickTensorBallBall _RELAX_SPIKES_MOTION /tmp/ fiber stick 0.0020500000000000002 41 402 1 fiber tensor 0.0015 0.00042999999999999999 0.00042999999999999999 63 1764 2 non-fiber ball 0.00064999999999999997 68 1115 3 non-fiber ball 0.0028 885 4582 4 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp.bvals new file mode 100644 index 0000000..bf9b80d --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp.bvals @@ -0,0 +1 @@ +0 1000 2000 3000 0 1000 3000 2000 0 1000 2000 3000 0 \ No newline at end of file diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp.bvecs similarity index 100% copy from DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs copy to DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp.bvecs diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_MASK.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_MASK.nii.gz new file mode 100644 index 0000000..723e4d2 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_MASK.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME1.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME1.nii.gz new file mode 100644 index 0000000..bfc4eef Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME1.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME2.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME2.nii.gz new file mode 100644 index 0000000..499cb70 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME2.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME3.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME3.nii.gz new file mode 100644 index 0000000..5a313a7 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME3.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME4.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME4.nii.gz new file mode 100644 index 0000000..d59ebf9 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp_VOLUME4.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.bvals new file mode 100644 index 0000000..bf9b80d --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.bvals @@ -0,0 +1 @@ +0 1000 2000 3000 0 1000 3000 2000 0 1000 2000 3000 0 \ No newline at end of file diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.bvecs similarity index 64% copy from DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs copy to DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.bvecs index 142a43c..09a4cc9 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.bvecs @@ -1,3 +1,3 @@ 0 1 1 1 0 0 0 0 0 0 0 0 0 -0 0 0 0 0 1 1 1 0 0 0 0 0 +0 0 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.nii.gz new file mode 100644 index 0000000..e8cd1a6 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp similarity index 83% copy from DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp copy to DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp index b2a1020..a29ccfd 100644 --- a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp @@ -1,145 +1,147 @@ 0 0.10000000000000001 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true false false true - 196 - 254 - 11 + 72 + 87 + 1 - 0.699999988 - 0.699999988 - 0.699999988 + 2.5 + 2.5 + 2.5 - 68.1999969 - 104.300003 - 11.999999 + -90.625 + 125.375 + 16.125 - -1 + 1 0 0 0 -1 0 0 0 1 - 0 + 1 0 1 false 0.75 - 7828.38916 - 5520 + 500 + 100 + 3119 921 - 90 + 30 1 50 true 0 true false 5 1 0.397000015 - 0.0199999996 + 0.0016 70 1 0.0649999976 false true 5 0 0 0 0 10 random false - false + 0 + true false false false false false false false true StickTensorBallBall - _RELAX_SPIKES_MOTION + _RELAX_COMPLEX-GAUSSIAN-500 /tmp/ fiber stick 0.0020500000000000002 - 41 - 402 + 80 + 780 1 fiber tensor 0.0015 0.00042999999999999999 0.00042999999999999999 - 63 - 1764 + 80 + 780 2 non-fiber ball 0.00064999999999999997 68 1115 3 non-fiber ball 0.0028 885 - 4582 + 4500 4 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp.bvals new file mode 100644 index 0000000..a96ce03 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp.bvals @@ -0,0 +1 @@ +0 \ No newline at end of file diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp.bvecs new file mode 100644 index 0000000..c130fb1 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp.bvecs @@ -0,0 +1,3 @@ +0 +0 +0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_MASK.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_MASK.nii.gz new file mode 100644 index 0000000..723e4d2 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_MASK.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME1.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME1.nii.gz new file mode 100644 index 0000000..bfc4eef Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME1.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME2.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME2.nii.gz new file mode 100644 index 0000000..499cb70 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME2.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME3.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME3.nii.gz new file mode 100644 index 0000000..5a313a7 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME3.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME4.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME4.nii.gz new file mode 100644 index 0000000..d59ebf9 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp_VOLUME4.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.bvals new file mode 100644 index 0000000..a96ce03 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.bvals @@ -0,0 +1 @@ +0 \ No newline at end of file diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.bvecs new file mode 100644 index 0000000..c130fb1 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.bvecs @@ -0,0 +1,3 @@ +0 +0 +0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.nii.gz new file mode 100644 index 0000000..a1706a4 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/param1.dwi b/DiffusionImaging/Fiberfox/params/param1.dwi index 376fdce..d270262 100644 Binary files a/DiffusionImaging/Fiberfox/params/param1.dwi and b/DiffusionImaging/Fiberfox/params/param1.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param1.ffp b/DiffusionImaging/Fiberfox/params/param1.ffp index d3645c0..a8701eb 100644 --- a/DiffusionImaging/Fiberfox/params/param1.ffp +++ b/DiffusionImaging/Fiberfox/params/param1.ffp @@ -1,185 +1,185 @@ 0 0.1 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true true false true 20 20 3 2 2 2 0 0 0 <1>1 <2>0 <3>0 <4>0 <5>1 <6>0 <7>0 <8>0 <9>1 6 <0> 0 0 0 <1> 6.123233995736766e-17 0 1 <2> -0.1193090531219969 0.5624445414792704 0.8181818181818182 <3> -0.7709122804136979 0.02712154533579388 0.6363636363636364 <4> -0.3931120931892352 -0.7992817475336491 0.4545454545454548 <5> 0.5484321238232369 -0.7904695062236604 0.2727272727272728 <6> 0.9938620722844124 0.06303743700862478 0.09090909090909105 0 1 2 true 1 177 4000 100 100 1 50 1000 true 0 0 30 true false 10 1 0.25 - 0.01 + 0.0016 70 0.75 true true true 10 0 0 0 0 15 random true true true true true true false true StickZeppelinBallAstrosticks _RELAX_GHOST_ALIASING_SPIKES_RINGING_DISTORTED_EDDY_MOTION_COMPLEX-GAUSSIAN-177 <0> fiber stick 0.001 110 780 1 <1> fiber tensor 0.001 0.00025 0.00025 110 780 2 <2> non-fiber ball 0.001 80 920 3 <3> non-fiber astrosticks 0.001 80 920 true 4 diff --git a/DiffusionImaging/Fiberfox/params/param2.dwi b/DiffusionImaging/Fiberfox/params/param2.dwi index ce47482..92fc3d5 100644 Binary files a/DiffusionImaging/Fiberfox/params/param2.dwi and b/DiffusionImaging/Fiberfox/params/param2.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param3.dwi b/DiffusionImaging/Fiberfox/params/param3.dwi index c33a080..977ec63 100644 Binary files a/DiffusionImaging/Fiberfox/params/param3.dwi and b/DiffusionImaging/Fiberfox/params/param3.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param4.dwi b/DiffusionImaging/Fiberfox/params/param4.dwi index da628b5..db4ded6 100644 Binary files a/DiffusionImaging/Fiberfox/params/param4.dwi and b/DiffusionImaging/Fiberfox/params/param4.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param5.dwi b/DiffusionImaging/Fiberfox/params/param5.dwi index 8400aa7..5ce8d7e 100644 Binary files a/DiffusionImaging/Fiberfox/params/param5.dwi and b/DiffusionImaging/Fiberfox/params/param5.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param6.dwi b/DiffusionImaging/Fiberfox/params/param6.dwi index 3605f99..8f71ede 100644 Binary files a/DiffusionImaging/Fiberfox/params/param6.dwi and b/DiffusionImaging/Fiberfox/params/param6.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param7.dwi b/DiffusionImaging/Fiberfox/params/param7.dwi index 9876587..2dce829 100644 Binary files a/DiffusionImaging/Fiberfox/params/param7.dwi and b/DiffusionImaging/Fiberfox/params/param7.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param8.dwi b/DiffusionImaging/Fiberfox/params/param8.dwi index 85e6029..1689474 100644 Binary files a/DiffusionImaging/Fiberfox/params/param8.dwi and b/DiffusionImaging/Fiberfox/params/param8.dwi differ diff --git a/DiffusionImaging/Fiberfox/params/param8.ffp b/DiffusionImaging/Fiberfox/params/param8.ffp index eaa4c18..df17ed0 100644 --- a/DiffusionImaging/Fiberfox/params/param8.ffp +++ b/DiffusionImaging/Fiberfox/params/param8.ffp @@ -1,166 +1,166 @@ 0 0.1 100 1 0 0 0 0 0 0 0 0 0 1 1 1 true true false true 20 20 3 2 2 2 0 0 0 <1>1 <2>0 <3>0 <4>0 <5>1 <6>0 <7>0 <8>0 <9>1 6 <0> 0 0 0 <1> 6.123233995736766e-17 0 1 <2> -0.1193090531219969 0.5624445414792704 0.8181818181818182 <3> -0.7709122804136979 0.02712154533579388 0.6363636363636364 <4> -0.3931120931892352 -0.7992817475336491 0.4545454545454548 <5> 0.5484321238232369 -0.7904695062236604 0.2727272727272728 <6> 0.9938620722844124 0.06303743700862478 0.09090909090909105 0 0 1 false 0.6000000000000001 0 4000 100 100 1 50 3000 true 0 0 30 true false 0 1 0 - 0.1 + 0.002 70 1 false false true 10 0 0 0 0 15 random false false false false true false false true StickBall _RELAX_EDDY <0> fiber stick 0.001 110 780 1 <1> non-fiber ball 0.001 80 920 3 diff --git a/DiffusionImaging/Fiberfox/params/param9.dwi b/DiffusionImaging/Fiberfox/params/param9.dwi index da28c7a..10f2c08 100644 Binary files a/DiffusionImaging/Fiberfox/params/param9.dwi and b/DiffusionImaging/Fiberfox/params/param9.dwi differ