diff --git a/DiffusionImaging/Fiberfox/SignalGen_BrainSlice.fib b/DiffusionImaging/Fiberfox/SignalGen_BrainSlice.fib new file mode 100644 index 0000000..9e2ffcc Binary files /dev/null and b/DiffusionImaging/Fiberfox/SignalGen_BrainSlice.fib differ diff --git a/DiffusionImaging/Fiberfox/SignalGen_BrainSliceTemplate.nii.gz b/DiffusionImaging/Fiberfox/SignalGen_BrainSliceTemplate.nii.gz new file mode 100644 index 0000000..b297adb Binary files /dev/null and b/DiffusionImaging/Fiberfox/SignalGen_BrainSliceTemplate.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_1.bvals new file mode 100644 index 0000000..bf9b80d --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1.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.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_1.bvecs new file mode 100644 index 0000000..142a43c --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1.bvecs @@ -0,0 +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 0 0 0 0 1 1 1 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp new file mode 100644 index 0000000..b2a1020 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp @@ -0,0 +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 + 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.ffp.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp.bvals new file mode 100644 index 0000000..d3bf7a3 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp.bvals @@ -0,0 +1 @@ +0 1000 2000 3000 0 1000 3000 2000 0 1000 2000 3000 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp.bvecs new file mode 100644 index 0000000..a6bc78f --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp.bvecs @@ -0,0 +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 0 0 0 0 1 1 1 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_MASK.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_MASK.nii.gz new file mode 100644 index 0000000..723e4d2 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_MASK.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME1.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME1.nii.gz new file mode 100644 index 0000000..bfc4eef Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME1.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME2.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME2.nii.gz new file mode 100644 index 0000000..499cb70 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME2.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME3.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME3.nii.gz new file mode 100644 index 0000000..5a313a7 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME3.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME4.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME4.nii.gz new file mode 100644 index 0000000..d59ebf9 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp_VOLUME4.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvals new file mode 100644 index 0000000..bf9b80d --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1_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_1_OUT.bvecs new file mode 100644 index 0000000..142a43c --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.bvecs @@ -0,0 +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 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 new file mode 100644 index 0000000..4b65a8a Binary files /dev/null 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 new file mode 100644 index 0000000..835b424 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp @@ -0,0 +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 + 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.ffp.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp.bvals new file mode 100644 index 0000000..d3bf7a3 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp.bvals @@ -0,0 +1 @@ +0 1000 2000 3000 0 1000 3000 2000 0 1000 2000 3000 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp.bvecs new file mode 100644 index 0000000..a6bc78f --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp.bvecs @@ -0,0 +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 0 0 0 0 1 1 1 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_MASK.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_MASK.nii.gz new file mode 100644 index 0000000..723e4d2 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_MASK.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME1.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME1.nii.gz new file mode 100644 index 0000000..bfc4eef Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME1.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME2.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME2.nii.gz new file mode 100644 index 0000000..499cb70 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME2.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME3.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME3.nii.gz new file mode 100644 index 0000000..5a313a7 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME3.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME4.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME4.nii.gz new file mode 100644 index 0000000..d59ebf9 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp_VOLUME4.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.bvals new file mode 100644 index 0000000..bf9b80d --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_2_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_2_OUT.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.bvecs new file mode 100644 index 0000000..142a43c --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.bvecs @@ -0,0 +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 0 0 0 0 1 1 1 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz new file mode 100644 index 0000000..515b33b Binary files /dev/null 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 new file mode 100644 index 0000000..70fe67c --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp @@ -0,0 +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 + 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.ffp.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp.bvals new file mode 100644 index 0000000..ed52bc6 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp.bvals @@ -0,0 +1 @@ +0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp.bvecs new file mode 100644 index 0000000..144c287 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp.bvecs @@ -0,0 +1,3 @@ +0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp_MASK.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp_MASK.nii.gz new file mode 100644 index 0000000..723e4d2 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp_MASK.nii.gz differ diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp_VOLUME1.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp_VOLUME1.nii.gz new file mode 100644 index 0000000..bfc4eef Binary files /dev/null and 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a/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.bvals b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.bvals new file mode 100644 index 0000000..4c57367 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.bvals @@ -0,0 +1 @@ +0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.bvecs b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.bvecs new file mode 100644 index 0000000..0845a2e --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.bvecs @@ -0,0 +1,3 @@ +0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.log b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.log new file mode 100644 index 0000000..b19ab90 --- /dev/null +++ b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.log @@ -0,0 +1,41 @@ +Logfile: /home/neher/mitk/mitkdata/DiffusionImaging/Fiberfox//BrainSlice_3.log +0:0:0 > Starting Fiberfox dMRI simulation +Output image spacing: [2.5,2.5,2.5] +Output image size: [72,87,1] +Working image spacing: [2.5,2.5,2.5] +Working image size: [72,87,1] +Resampling tissue mask +Using tissue mask +Using volume fraction map for fiber compartment 1 +Using volume fraction map for fiber compartment 2 +Using volume fraction map for non-fiber compartment 1 +Using volume fraction map for non-fiber compartment 2 + +Setting fiber radius to 77.22µm to obtain full voxel. + +0:0:0 > Generating 4-compartment diffusion-weighted signal. +b-values: 0 +Volumes: 13 + + +0% 10 20 30 40 50 60 70 80 90 100% +|----|----|----|----|----|----|----|----|----|----| +*************************************************** + + +0:0:0 > Simulating k-space acquisition using 1 coil(s) +Acquisition type: single shot EPI +Simulating signal relaxation +Parallel volumes: 4 +Threads per slice: 4 +0% 10 20 30 40 50 60 70 80 90 100% +|----|----|----|----|----|----|----|----|----|----| +*************************************************** + +0:0:7 > Finalizing image +Adding signal drift: 0.0649999976 +0% 10 20 30 40 50 60 70 80 90 100% +|----|----|----|----|----|----|----|----|----|----| +*************************************************** + +0:0:7 > Finished simulation diff --git a/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz new file mode 100644 index 0000000..dea5053 Binary files /dev/null and b/DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz differ