diff --git a/content/01-pyafq.ipynb b/content/01-pyafq.ipynb index b0e2496..45a035c 100644 --- a/content/01-pyafq.ipynb +++ b/content/01-pyafq.ipynb @@ -41,20 +41,14 @@ "import os\n", "import os.path as op\n", "\n", + "home = op.expanduser(\"~\")\n", "pwd = op.dirname(os.getcwd())\n", "\n", - "os.environ[\"TEMPLATEFLOW_HOME\"] = op.join(pwd, \"..\", \"data_\", \"tractometry\")\n", - "os.environ[\"DIPY_HOME\"] = op.join(pwd, \"..\", \"data_\", \"tractometry\")\n", - "os.environ[\"AFQ_HOME\"] = op.join(pwd, \"..\", \"data_\", \"tractometry\")\n" + "os.environ[\"TEMPLATEFLOW_HOME\"] = op.join(home, \"data_\", \"tractometry\")\n", + "os.environ[\"DIPY_HOME\"] = op.join(home, \"data_\", \"tractometry\")\n", + "os.environ[\"AFQ_HOME\"] = op.join(home, \"data_\", \"tractometry\")\n" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - }, { "cell_type": "code", "execution_count": null, @@ -129,10 +123,13 @@ "\n", "```{alert}\n", "\n", - "Running the code below triggers the full pipeline of operations leading to the\n", - "computation of the tract profiles. Therefore, it takes a little while to run\n", - "(about 10 minutes, typically)\n", - "\n", + "For the purpose of the neurolibre preprint, the pipeline has been run in \n", + "advance and cached in the data folder (under `data/tractometry`). In \n", + "usual practice, the following line of code would trigger the full computational\n", + "pipeline, which takes about 10 minutes to run and requires more RAM than \n", + "is available through the neurolibre server. However, the caching behavior \n", + "is typical to pyAFQ. Once derivatives are computed, they are cached such that \n", + "they can be reused. \n", "```\n" ] },