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Merge pull request #165 from jhlegarreta/ImproveStyle
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STYLE: Improve style
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@jhlegarreta
jhlegarreta authored Jul 19, 2021
2 parents 99d17dd + bcfcf06 commit 73bb0d4
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64 changes: 32 additions & 32 deletions _episodes/introduction.md
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Expand Up @@ -76,8 +76,8 @@ tree '../data/ds000221'
├── sub-010001/
└── sub-010002/
├── ses-01/
│    ├── anat
   │   │ ├── sub-010002_ses-01_acq-lowres_FLAIR.json
│ ├── anat
│ │ ├── sub-010002_ses-01_acq-lowres_FLAIR.json
│ │ ├── sub-010002_ses-01_acq-lowres_FLAIR.nii.gz
│ │ ├── sub-010002_ses-01_acq-mp2rage_defacemask.nii.gz
│ │ ├── sub-010002_ses-01_acq-mp2rage_T1map.nii.gz
Expand All @@ -88,37 +88,37 @@ tree '../data/ds000221'
│ │ ├── sub-010002_ses-01_inv-2_mp2rage.nii.gz
│ │ ├── sub-010002_ses-01_T2w.json
│ │ └── sub-010002_ses-01_T2w.nii.gz
   │ ├── dwi
   │    │ ├── sub-010002_ses-01_dwi.bval
   │    │ │── sub-010002_ses-01_dwi.bvec
   │    │ │── sub-010002_ses-01_dwi.json
   │    │ └── sub-010002_ses-01_dwi.nii.gz
  │ ├── fmap
   │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.json
  │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.nii.gz
   │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.json
  │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.nii.gz
   │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.json
  │    │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.nii.gz
   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json
  │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json
  │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.json
  │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.json
  │    │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json
  │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json
  │    │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.json
  │    │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.nii.gz
   │    │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.json
  │    │ └── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.nii.gz
│ ├── dwi
│ │ ├── sub-010002_ses-01_dwi.bval
│ │ │── sub-010002_ses-01_dwi.bvec
│ │ │── sub-010002_ses-01_dwi.json
│ │ └── sub-010002_ses-01_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.json
│ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude1.nii.gz
│ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.json
│ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_magnitude2.nii.gz
│ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.json
│ │ ├── sub-010002_ses-01_acq-GEfmap_run-01_phasediff.nii.gz
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.json
│ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-AP_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.json
│ │ ├── sub-010002_ses-01_acq-sefmapBOLDpre_dir-PA_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.json
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-AP_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.json
│ │ ├── sub-010002_ses-01_acq-SEfmapBOLDpost_dir-PA_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.json
│ │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-AP_epi.nii.gz
│ │ ├── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.json
│ │ └── sub-010002_ses-01_acq-SEfmapDWI_dir-PA_epi.nii.gz
│ └── func
   │    │ ├── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.json
  │    │ └── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.nii.gz
│ │ ├── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.json
│ │ └── sub-010002_ses-01_task-rest_acq-AP_run-01_bold.nii.gz
└── ses-02/
~~~
{: .output}
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66 changes: 33 additions & 33 deletions code/introduction/introduction.ipynb
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Expand Up @@ -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",
" │ └── func\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 Down Expand Up @@ -357,4 +357,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
}
}
66 changes: 33 additions & 33 deletions code/introduction/solutions/introduction_solutions.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
" │ └── func\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 Down Expand Up @@ -516,4 +516,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
}
}
2 changes: 1 addition & 1 deletion index.md
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Expand Up @@ -26,7 +26,7 @@ and teaching experience.
signal or image is represented digitally, an entry-level knowledge about aspects
linked to medical image analysis, and a minimal set of computing and programming
skills to install the required tools and to follow the lesson ([see the
BIDS-dMRI Setup page](https://carpentries-incubator.github.io/SDC-BIDS-dMRI/setup.html).
BIDS-dMRI Setup page](https://carpentries-incubator.github.io/SDC-BIDS-dMRI/setup.html)).
This lesson requires learners to have completed the [Introduction to MRI and BIDS carpentry](https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/)
corresponding to the Neuroimaging Curriculum.
{: .prereq}
Expand Down

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