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Merged
merged 2 commits into from
Jul 23, 2024
Merged

fixed some spelling #51

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496e4c0
fixed some spelling
evamariie Jun 16, 2024
d25f493
Merge branch 'main' into evamariie-patch-2
MarcelRosier Jul 23, 2024
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16 changes: 8 additions & 8 deletions BraTS-Toolkit/glioma_segmentation_with_BraTS_Toolkit.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
"source": [
"# Warning\n",
"\n",
"This tutorial is a work in progress, it does not cover all the functionalities yet. However, it will give you a good overview how you can generate tumor segmentations with BraTS Toolkit.\n"
"This tutorial is a work in progress, it does not cover all the functionalities yet. However, it will give you a good overview of how you can generate tumor segmentations with BraTS Toolkit.\n"
]
},
{
Expand All @@ -28,13 +28,13 @@
"2. **Import** of raw data (cMRI)\n",
" \n",
" \n",
"3. **Preprocessing via BrainLes preprocessig package** instead of vanilla preprocessing pipeline from BraTS Toolkit. BraTS challenge algorithms expect preprocessed files (co-registered, skullstripped in SRI-24 space)\n",
"3. **Preprocessing via BrainLes preprocessing package** instead of vanilla preprocessing pipeline from BraTS Toolkit. BraTS challenge algorithms expect preprocessed files (co-registered, skullstripped in SRI-24 space)\n",
" \n",
" \n",
"4. **Segmentation with BraTS Toolkit** \n",
" \n",
" \n",
"5. **Fusion** of generated segementations \n",
"5. **Fusion** of generated segmentations \n",
"\n"
]
},
Expand All @@ -55,10 +55,10 @@
"optional (but recommended):\n",
"\n",
"- CUDA drivers\n",
"- a GPU that is supported (each algorithms supports different set of GPUs)\n",
"- a GPU that is supported (each algorithm supports different set of GPUs)\n",
"<!-- TODO specify -->\n",
"\n",
"Run the subsequent cell to check CUDA availability, your python and docker version. "
"Run the subsequent cell to check CUDA availability, your Python and docker version. "
]
},
{
Expand Down Expand Up @@ -206,14 +206,14 @@
"source": [
"## 2. Import raw input data\n",
"\n",
"Raw imput data require\n",
"Raw input data require\n",
"- exam with skull and 4 sequences (T1, T1c, T2, T2-FLAIR), only one file each (in total 4 files) \n",
" - file names must end with \"*t1.nii.gz\", \"*t1c.nii.gz\", \"*t2.nii.gz\" and \"*fla.nii.gz\"\n",
" - [Nifti \".nii.gz\"](https://brainder.org/2012/09/23/the-nifti-file-format/) file type \n",
"- each exam (4 files) needs to be places in an individual folder within the data folder \n",
"```<this repository>/BraTS-Toolkit/data/```. \n",
"\n",
"The structure is shown using two example exams:\n",
"The structure is shown using two examples exams:\n",
"```\n",
"BraTS-Toolkit\n",
"├── data\n",
Expand Down Expand Up @@ -297,7 +297,7 @@
"source": [
"## 3. Preprocessing\n",
"\n",
"BraTS challenge algorithms expect co-registered, skullstripped files in SRI-24 space, to achieve this preprocessing is required.\n",
"BraTS challenge algorithms expect co-registered, skull-stripped files in SRI-24 space, to achieve this preprocessing is required.\n",
"Instead of using the vanilla preprocessing pipeline from BraTS Toolkit, we recommend using the new [BrainLes preprocessing package](https://github.com/BrainLesion/preprocessing/tree/main/brainles_preprocessing).\n"
]
},
Expand Down