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‎notebooks/introduction_dataset.ipynb

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"\n",
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"The dataset for this tutorial is coming from [https://openfmri.org/](https://openfmri.org/), a homepage dedicated to the free and open sharing of raw magnetic resonance imaging (MRI) datasets. We already downloaded the dataset [ds000114](https://github.com/datalad/ds000114) into the data folder at the current location. To reduce the size of the total dataset, only the first two subjects (`sub-01` and `sub-02`) were kept.\n",
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"\n",
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"So let's have a look at the tutorial dataset for `sub-01`."
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"So let's have a look at the tutorial dataset."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 4,
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"deletable": true,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"/data/ds000114/sub-01/\r\n",
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"├── anat\r\n",
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"│   └── sub-01_T1w.nii.gz -> ../../.git/annex/objects/QP/jm/MD5E-s8677710--d6820f6cb8fb965e864419c14f6a22d5.nii.gz/MD5E-s8677710--d6820f6cb8fb965e864419c14f6a22d5.nii.gz\r\n",
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"├── dwi\r\n",
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"│   └── sub-01_dwi.nii.gz -> ../../.git/annex/objects/X2/kJ/MD5E-s104193417--454850ac9ed1c96c40b6b7946e51bf71.nii.gz/MD5E-s104193417--454850ac9ed1c96c40b6b7946e51bf71.nii.gz\r\n",
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"└── func\r\n",
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" ├── sub-01_task-fingerfootlips_bold.nii.gz -> ../../.git/annex/objects/k6/4f/MD5E-s24454931--e9ab535d84a922b0c7ed52461244cf47.nii.gz/MD5E-s24454931--e9ab535d84a922b0c7ed52461244cf47.nii.gz\r\n",
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" ├── sub-01_task-linebisection_bold.nii.gz -> ../../.git/annex/objects/32/Qq/MD5E-s31617092--151bc230c3b577110883369b6fad0daa.nii.gz/MD5E-s31617092--151bc230c3b577110883369b6fad0daa.nii.gz\r\n",
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" └── sub-01_task-linebisection_events.tsv\r\n",
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"/data/ds000114/\r\n",
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"├── dataset_description.json\r\n",
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"├── derivatives\r\n",
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"│   └── freesurfer\r\n",
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"│   ├── sub-01\r\n",
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"│   ├── sub-02\r\n",
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"│   └── Untitled1.ipynb\r\n",
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"├── dwi.bval\r\n",
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"├── dwi.bvec\r\n",
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"├── sub-01\r\n",
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"│   ├── anat\r\n",
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"│   │   └── sub-01_T1w.nii.gz -> ../../.git/annex/objects/QP/jm/MD5E-s8677710--d6820f6cb8fb965e864419c14f6a22d5.nii.gz/MD5E-s8677710--d6820f6cb8fb965e864419c14f6a22d5.nii.gz\r\n",
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"│   ├── dwi\r\n",
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"│   │   └── sub-01_dwi.nii.gz -> ../../.git/annex/objects/X2/kJ/MD5E-s104193417--454850ac9ed1c96c40b6b7946e51bf71.nii.gz/MD5E-s104193417--454850ac9ed1c96c40b6b7946e51bf71.nii.gz\r\n",
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"│   └── func\r\n",
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"│   ├── sub-01_task-fingerfootlips_bold.nii.gz -> ../../.git/annex/objects/k6/4f/MD5E-s24454931--e9ab535d84a922b0c7ed52461244cf47.nii.gz/MD5E-s24454931--e9ab535d84a922b0c7ed52461244cf47.nii.gz\r\n",
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"│   ├── sub-01_task-linebisection_bold.nii.gz -> ../../.git/annex/objects/32/Qq/MD5E-s31617092--151bc230c3b577110883369b6fad0daa.nii.gz/MD5E-s31617092--151bc230c3b577110883369b6fad0daa.nii.gz\r\n",
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"│   └── sub-01_task-linebisection_events.tsv\r\n",
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"├── sub-02\r\n",
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"│   ├── anat\r\n",
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"│   │   └── sub-02_T1w.nii.gz -> ../../.git/annex/objects/qq/gm/MD5E-s10025785--0e790e210a275d76e3f2f4d895df6358.nii.gz/MD5E-s10025785--0e790e210a275d76e3f2f4d895df6358.nii.gz\r\n",
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"│   ├── dwi\r\n",
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"│   │   └── sub-02_dwi.nii.gz -> ../../.git/annex/objects/8x/vp/MD5E-s104222416--86575d07809e9c717079592a12c69344.nii.gz/MD5E-s104222416--86575d07809e9c717079592a12c69344.nii.gz\r\n",
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"│   └── func\r\n",
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"│   ├── sub-02_task-fingerfootlips_bold.nii.gz -> ../../.git/annex/objects/pG/k1/MD5E-s24882575--75c39bee9e25e02c629dfcce1b378589.nii.gz/MD5E-s24882575--75c39bee9e25e02c629dfcce1b378589.nii.gz\r\n",
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"│   ├── sub-02_task-linebisection_bold.nii.gz -> ../../.git/annex/objects/WM/m9/MD5E-s32248732--4cd877de7b4c66e073610dffb67dfbcc.nii.gz/MD5E-s32248732--4cd877de7b4c66e073610dffb67dfbcc.nii.gz\r\n",
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"│   └── sub-02_task-linebisection_events.tsv\r\n",
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"├── task-fingerfootlips_bold.json\r\n",
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"├── task-fingerfootlips_events.tsv\r\n",
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"└── task-linebisection_bold.json\r\n",
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"\r\n",
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"3 directories, 5 files\r\n"
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"12 directories, 17 files\r\n"
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]
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}
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],
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"source": [
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"!tree /data/ds000114/sub-01/"
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"!tree -L 3 /data/ds000114/"
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]
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},
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{
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"editable": true
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"source": [
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"As you can, we have one anatomical T1w image, two functional images, `fingerfootlips` and `linebisection`, and one diffusion weighted image. "
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"As you can, for every subject we have one anatomical T1w image, two functional images, `fingerfootlips` and `linebisection`, and one diffusion weighted image. In addition, we have directory with derivatives. \n",
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"\n",
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"If you used `datalad` or `git annex` to get the dataset, you can see symlinks for the image files."
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]
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{
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},
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{
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