Added some FAQ info + removed cluster-specific path

examples/tutorial.ipynb

@@ -41,7 +41,11 @@
    "source": [
     "# Importing Data\n",
     "\n",
-    "We can use `dials.import` as a way to import the data files written at experimental facilities into a format that is friendly to both `DIALS` and `laue-dials`. Feel free to use any data set you'd like below, but a [sample lysozyme data set](https://zenodo.org/record/6407157) has been uploaded to zenodo for your convenience, and this notebook has been tested using that dataset."
+    "We can use `dials.import` as a way to import the data files written at experimental facilities into a format that is friendly to both `DIALS` and `laue-dials`. Feel free to use any data set you'd like below, but a [sample lysozyme data set](https://zenodo.org/record/6407157) has been uploaded to zenodo for your convenience, and this notebook has been tested using that dataset.\n",
+    "\n",
+    "### Masks\n",
+    "\n",
+    "Note that if you make a mask later in the pipeline (using `dials.image_viewer` or any other tool), you will need to either return to this step and use the `lookup.mask=\"FILENAME\"` option or use `dials.apply_mask` to files prior to running `laue.predict`."
    ]
   },
   {
@@ -64,7 +68,7 @@
     "    geometry.beam.wavelength=1.04 \\\n",
     "    geometry.detector.panel.pixel=0.08854,0.08854 \\\n",
     "    lookup.mask=\"pixels.mask\" \\\n",
-    "    input.template=\"/n/hekstra_lab/data/201903xx_APS_BioCARS/e080/e080_###.mccd\"  #\"PATH/TO/DATA/e080_###.mccd\" # Replace with the path to your raw data"
+    "    input.template=\"PATH/TO/DATA/e080_###.mccd\" # Replace with the path to your raw data"
    ]
   },
   {
@@ -106,7 +110,7 @@
    "source": [
     "# Viewing Images\n",
     "\n",
-    "Sometimes it's helpful to be able to see the analysis data overlayed on the raw data. DIALS has a utility for viewing spot information on the raw images called `dials.image_viewer`. For example, the spotfinding gain parameter can be tuned to capture more spots, but increasing too much finds nonexistent spots. To check this, we can use the image viewer to see what spots were found on images. We need to provide an `expt` file and a `refl` file -- the `imported.expt` and `strong.refl` files will do for checking spotfinding. This program also has utilities for generating masks if they are needed."
+    "Sometimes it's helpful to be able to see the analysis data overlayed on the raw data. DIALS has a utility for viewing spot information on the raw images called `dials.image_viewer`. For example, the spotfinding gain parameter can be tuned to capture more spots, but increasing too much finds nonexistent spots. To check this, we can use the image viewer to see what spots were found on images. We need to provide an `expt` file and a `refl` file -- the `imported.expt` and `strong.refl` files will do for checking spotfinding. This program also has utilities for generating masks if they are needed. The red dots from the checkbox \"Mark centers of mass\" are the spots found by `laue.initial_solution` (which in turn makes a call to `dials.find_spots`). These are best used for judging whether you need to adjust the gain higher (for fewer spots) or lower (for more) during spotfinding. You can find more details on the image viewer in the [DIALS tutorial here](https://dials.github.io/documentation/tutorials/processing_in_detail_betalactamase.html)."
    ]
   },
   {