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@iishiishii
iishiishii committed Nov 27, 2024
1 parent 734f6b5 commit 5b54927
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84 changes: 56 additions & 28 deletions _sources/mrtrix3tissue.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
"source": [
"# MRtrix3Tissue\n",
"\n",
"Author: Thuy Dao\n",
"Author: Thuy Dao, Monika Doerig\n",
"\n",
"Citation: 3tissue.github.io/about.html"
]
Expand Down Expand Up @@ -134,7 +134,9 @@
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": true,
"tags": [
"output_scroll"
],
"vscode": {
"languageId": "plaintext"
}
Expand Down Expand Up @@ -284,9 +286,11 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {
"scrolled": true
"tags": [
"output_scroll"
]
},
"outputs": [
{
Expand All @@ -304,9 +308,10 @@
}
],
"source": [
"!mrconvert ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-AP_dwi.nii.gz AP.mif -fslgrad ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-AP_dwi.bvec ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-AP_dwi.bval\n",
"!mrconvert ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-PA_dwi.nii.gz PA.mif\n",
"!mrconvert PA.mif -fslgrad ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-PA_dwi.bvec ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-PA_dwi.bval - | mrmath - mean mean_b0_PA.mif -axis 3"
"%%bash\n",
"mrconvert ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-AP_dwi.nii.gz AP.mif -fslgrad ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-AP_dwi.bvec ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-AP_dwi.bval\n",
"mrconvert ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-PA_dwi.nii.gz PA.mif\n",
"mrconvert PA.mif -fslgrad ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-PA_dwi.bvec ds002080/sub-CON02/ses-postop/dwi/sub-CON02_ses-postop_acq-PA_dwi.bval - | mrmath - mean mean_b0_PA.mif -axis 3"
]
},
{
Expand All @@ -324,9 +329,11 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {
"scrolled": true
"tags": [
"output_scroll"
]
},
"outputs": [
{
Expand Down Expand Up @@ -409,8 +416,9 @@
}
],
"source": [
"!dwidenoise AP.mif dwi_denoised.mif -noise noise.mif\n",
"!mrdegibbs dwi_denoised.mif dwi_denoised_unringed.mif"
"%%bash\n",
"dwidenoise AP.mif dwi_denoised.mif -noise noise.mif\n",
"mrdegibbs dwi_denoised.mif dwi_denoised_unringed.mif"
]
},
{
Expand Down Expand Up @@ -463,7 +471,9 @@
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -513,7 +523,9 @@
"cell_type": "code",
"execution_count": 15,
"metadata": {
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -557,7 +569,9 @@
"cell_type": "code",
"execution_count": 16,
"metadata": {
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -622,7 +636,9 @@
"cell_type": "code",
"execution_count": 17,
"metadata": {
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -701,7 +717,11 @@
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"metadata": {
"tags": [
"scroll-output"
]
},
"outputs": [
{
"name": "stdout",
Expand Down Expand Up @@ -758,7 +778,9 @@
"jupyter": {
"outputs_hidden": true
},
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -1143,9 +1165,11 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": null,
"metadata": {
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -1196,9 +1220,10 @@
}
],
"source": [
"!mrconvert wmfod_norm.mif -coord 3 0 -axes 0,1,2 - | mrcalc csf_norm.mif gm_norm.mif - -add 5 -mult -gt csf_mask1.mif -datatype bit\n",
"!mrthreshold csf_norm.mif csf_mask2.mif -abs 0.141047\n",
"!mrcalc csf_mask1.mif csf_mask2.mif -mult csf_maskcombined.mif -datatype bit"
"%%bash\n",
"mrconvert wmfod_norm.mif -coord 3 0 -axes 0,1,2 - | mrcalc csf_norm.mif gm_norm.mif - -add 5 -mult -gt csf_mask1.mif -datatype bit\n",
"mrthreshold csf_norm.mif csf_mask2.mif -abs 0.141047\n",
"mrcalc csf_mask1.mif csf_mask2.mif -mult csf_maskcombined.mif -datatype bit"
]
},
{
Expand Down Expand Up @@ -1231,9 +1256,11 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": null,
"metadata": {
"scrolled": true
"tags": [
"scroll-output"
]
},
"outputs": [
{
Expand Down Expand Up @@ -1284,10 +1311,11 @@
}
],
"source": [
"!mrconvert dwi_denoised_unringed_preproc_unbiased_upsampled.mif reduced.mif -coord 3 $(cat bval_less_1000.txt)\n",
"!dwi2adc reduced.mif dwi_adc.mif\n",
"!mrconvert dwi_adc.mif extracted_adc.mif -coord 3 1\n",
"!!mrcalc extracted_adc.mif csf_maskcombined.mif -mult masked_adc.mif"
"%%bash\n",
"mrconvert dwi_denoised_unringed_preproc_unbiased_upsampled.mif reduced.mif -coord 3 $(cat bval_less_1000.txt)\n",
"dwi2adc reduced.mif dwi_adc.mif\n",
"mrconvert dwi_adc.mif extracted_adc.mif -coord 3 1\n",
"mrcalc extracted_adc.mif csf_maskcombined.mif -mult masked_adc.mif"
]
},
{
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