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STYLE: Improve style in introduction notebook #164

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STYLE: Improve style in introduction notebook #164

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e596a6e
STYLE: Change NBSP appearances to regular whitespaces
jhlegarreta Jul 9, 2021
bcbc697
STYLE: Remove trailing whitespaces
jhlegarreta Jul 9, 2021
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28 changes: 14 additions & 14 deletions code/introduction/introduction.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,14 +29,14 @@
"source": [
"## Dataset\n",
"\n",
"For the rest of this tutorial, we will make use of a subset of publicly available dataset, ds000030, from [openneuro.org](https://openneuro.org/datasets/ds000030) The dataset is structured according to the Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io/en/etable/)). "
"For the rest of this tutorial, we will make use of a subset of publicly available dataset, ds000030, from [openneuro.org](https://openneuro.org/datasets/ds000030) The dataset is structured according to the Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io/en/etable/))."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Below is a tree diagram showing the folder structure of a single MR session within ds000030. This was obtained by using the bash command `tree`. \n",
"Below is a tree diagram showing the folder structure of a single MR session within ds000030. This was obtained by using the bash command `tree`.\n",
"`!tree ../data/ds000030`\n",
"\n",
"```\n",
Expand All @@ -46,14 +46,14 @@
"├── dataset_description.json\n",
"├── README\n",
"└── sub-10788/\n",
"    ├── anat\n",
"    │   ├── sub-10788_T1w.json\n",
"    │   └── sub-10788_T1w.nii.gz\n",
"    └── dwi\n",
"       ├── sub-10788_dwi.bval\n",
"       │── sub-10788_dwi.bvec\n",
"       │── sub-10788_dwi.json\n",
"       └── sub-10788_dwi.nii.gz\n",
" ├── anat\n",
" │ ├── sub-10788_T1w.json\n",
" │ └── sub-10788_T1w.nii.gz\n",
" └── dwi\n",
" ├── sub-10788_dwi.bval\n",
" │── sub-10788_dwi.bvec\n",
" │── sub-10788_dwi.json\n",
" └── sub-10788_dwi.nii.gz\n",
"```"
]
},
Expand All @@ -77,7 +77,7 @@
"source": [
"## Querying a BIDS Dataset\n",
"\n",
"[`pybids`](https://bids-standard.github.io/pybids/) is a Python API for querying, summarizing and manipulating the BIDS folder structure. We will make use of `pybids` to query the necessary files. \n",
"[`pybids`](https://bids-standard.github.io/pybids/) is a Python API for querying, summarizing and manipulating the BIDS folder structure. We will make use of `pybids` to query the necessary files.\n",
"\n",
"Lets first pull the metadata from its associated JSON file using the `get_metadata()` function for the first run."
]
Expand Down Expand Up @@ -214,7 +214,7 @@
"\n",
"For this lesson, we will use the `Dipy` (Diffusion Imaging in Python) package for processing and analysing diffusion MRI.\n",
"\n",
"### Why `dipy`? \n",
"### Why `dipy`?\n",
"\n",
"- Fully free and open source\n",
"- Implemented in Python. Easy to understand, and easy to use.\n",
Expand Down Expand Up @@ -425,7 +425,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"We will need this gradient table later on to process our data and generate diffusion tensor images (DTI)! \n",
"We will need this gradient table later on to process our data and generate diffusion tensor images (DTI)!\n",
"\n",
"There is also a built in function for gradient tables, `b0s_mask` that can be used to separate diffusion weighted measurements from non-diffusion weighted measurements (b=0s/mm^2). Try to extract the vector corresponding to diffusion weighted measurements in the following cell!"
]
Expand Down Expand Up @@ -644,4 +644,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
}
}
72 changes: 36 additions & 36 deletions code/introduction/solutions/introduction_solutions.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
"source": [
"## Dataset\n",
"\n",
"For the rest of this tutorial, we will make use of a subset of publicly available dataset, ds000030, from [openneuro.org](https://openneuro.org/datasets/ds000030) The dataset is structured according to the Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io/en/etable/)). "
"For the rest of this tutorial, we will make use of a subset of publicly available dataset, ds000030, from [openneuro.org](https://openneuro.org/datasets/ds000030) The dataset is structured according to the Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io/en/etable/))."
]
},
{
Expand All @@ -53,8 +53,8 @@
"├── sub-010001/\n",
"└── sub-010002/\n",
" ├── ses-01/\n",
" │    ├── anat\n",
"    │   │ ├── sub-010002_ses-01_acq-lowres_FLAIR.json\n",
" │ ├── anat\n",
" │ │ ├── sub-010002_ses-01_acq-lowres_FLAIR.json\n",
" │ │ ├── sub-010002_ses-01_acq-lowres_FLAIR.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-mp2rage_defacemask.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-mp2rage_T1map.nii.gz\n",
Expand All @@ -65,37 +65,37 @@
" │ │ ├── sub-010002_ses-01_inv-2_mp2rage.nii.gz\n",
" │ │ ├── sub-010002_ses-01_T2w.json\n",
" │ │ └── sub-010002_ses-01_T2w.nii.gz\n",
"    │ ├── dwi\n",
"    │    │ ├── sub-010002_ses-01_dwi.bval\n",
"    │    │ │── sub-010002_ses-01_dwi.bvec\n",
"    │    │ │── sub-010002_ses-01_dwi.json\n",
"    │    │ └── sub-010002_ses-01_dwi.nii.gz\n",
"   │ ├── fmap\n",
"    │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.json\n",
"   │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.json\n",
"   │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.json\n",
"   │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.json\n",
"   │    │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.nii.gz\n",
"    │    │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.json\n",
"   │    │ └── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.nii.gz\n",
" │ ├── dwi\n",
" │ │ ├── sub-010002_ses-01_dwi.bval\n",
" │ │ │── sub-010002_ses-01_dwi.bvec\n",
" │ │ │── sub-010002_ses-01_dwi.json\n",
" │ │ └── sub-010002_ses-01_dwi.nii.gz\n",
" │ ├── fmap\n",
" │ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.json\n",
" │ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.json\n",
" │ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.json\n",
" │ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.json\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.nii.gz\n",
" │ │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.json\n",
" │ │ └── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.nii.gz\n",
" │ └── fmap\n",
"    │    │ ├── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.json\n",
"   │    │ └── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.nii.gz\n",
" │ │ ├── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.json\n",
" │ │ └── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.nii.gz\n",
" └── ses-02/\n",
" ```"
]
Expand All @@ -106,7 +106,7 @@
"source": [
"## Querying a BIDS Dataset\n",
"\n",
"[`pybids`](https://bids-standard.github.io/pybids/) is a Python API for querying, summarizing and manipulating the BIDS folder structure. We will make use of `pybids` to query the necessary files. \n",
"[`pybids`](https://bids-standard.github.io/pybids/) is a Python API for querying, summarizing and manipulating the BIDS folder structure. We will make use of `pybids` to query the necessary files.\n",
"\n",
"Lets first pull the metadata from its associated JSON file using the `get_metadata()` function for the first run."
]
Expand Down Expand Up @@ -154,7 +154,7 @@
"\n",
"For this lesson, we will use the `Dipy` (Diffusion Imaging in Python) package for processing and analysing diffusion MRI.\n",
"\n",
"### Why `dipy`? \n",
"### Why `dipy`?\n",
"\n",
"- Fully free and open source\n",
"- Implemented in Python. Easy to understand, and easy to use.\n",
Expand Down Expand Up @@ -238,7 +238,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"We will need this gradient table later on to process our data and generate diffusion tensor images (DTI)! \n",
"We will need this gradient table later on to process our data and generate diffusion tensor images (DTI)!\n",
"\n",
"There is also a built in function for gradient tables, `b0s_mask` that can be used to separate difussion weighted measurements from non-diffusion weighted measurements (b=0s/mm^2). Try to extract the vector corresponding to diffusion weighted measurements in the following cell!"
]
Expand Down