Update README with details about ISIS Data differences between 4.1 and earlier (#3985)

* Update installation instructions

* Update README.md

* Update README.md

* Updated based on feedback

README.md

@@ -303,11 +303,27 @@ This project uses a [Zenodo](https://zenodo.org) generated DOI. The badge at the
 
 Many ISIS applications require ancillary data. For example, calibration applications require flat files to do flat field corrections, and map projection applications require DTMs to accurately compute intersections. Due to its size, this data is stored in a separate directory called the ISIS Data Area. Any location can be used for the ISIS Data Area, the software simply requires that the ISISDATA environment variable is set to its location.
 
-### Structure of the ISIS3 Data Area
+### Structure of the ISIS Data Area
 
-Under the root directory of the ISIS Data Area pointed to by the ISISDATA environment variable are a variety of sub-directories. Each mission supported by ISIS has a sub-directory that contains mission specific processing data such as flat files and mission specific SPICE. There are also data areas used by more generic applications. These sub-directories contain everything from templates to test data.
+Under the root directory of the ISIS Data Area pointed to by the ISISDATA/ISIS3DATA environment variable are a variety of sub-directories. Each mission supported by ISIS has a sub-directory that contains mission specific processing data such as flat files and mission specific SPICE. There are also data areas used by more generic applications. These sub-directories contain everything from templates to test data.
 
-### Size of the ISIS3 Data Area
+### Versions of the ISIS Data Area
+
+In ISIS version 4.1.0, several files previously stored in the data area closely associated with ISIS applications were moved into version control with the ISIS source code. Additionally, the environment variables used for the ISIS Data Area and the rsync location for the ISIS Data Area were also updated. 
+
+The correct environment variable names and rsync modules to use for the ISIS Data Area for each version of ISIS are summarized in the table below:
+
+ISIS version | ISIS Data Environment variable name | ISIS Data rsync module
+---|---|---
+3.x | `$ISIS3DATA` | `isis3data`
+4.0.x | `$ISIS3DATA` | `isis3data`
+4.1.0 | `$ISISDATA` | `isisdata`
+
+The ISIS Data rsync module specifies where to rsync the data from and is the name used after the `::` in the rsync download commands below. For example, the rsync module is in bold in the following example rsync command:
+
+``rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::``**``isis3data``**``/data/`` .
+
+### Size of the ISIS Data Area
 
 If you plan to work with data from all missions, then the download will require about 520 GB for all the ancillary data. However, most of this volume is taken up by SPICE files. We have a [Web service](#isis-spice-web-service) that can be used in lieu of downloading all of the SPICE files. This reduces the total download size to about 10 GB.
 
@@ -315,14 +331,17 @@ If you plan to work with data from all missions, then the download will require
 
 The ISIS Data Area is hosted on rsync servers and not through conda channels like the ISIS binaries. This requires using the rsync command from within a terminal window within your Unix distribution, or from within WSL if running Windows 10.  Downloading all mission data requires over 520 GB of disk space. If you want to acquire only certain mission data [click here](#Mission-Specific-Data-Downloads). To download all ISIS data files, continue reading.
 
-To download all ISIS data, enter the following commands in the location where you want to install the ISIS Data Area:
+To download all ISIS data, enter the following commands in the location where you want to install the ISIS Data Area, for versions of ISIS 4.1.0 and later:
 
     cd $ISISDATA
     rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/ .
 
+For earlier versions, use: 
 
-> Note: The above command downloads all ISIS data including the required base data area and all of the optional mission data areas.
+    cd $ISIS3DATA
+    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/ .
 
+> Note: The above command downloads all ISIS data including the required base data area and all of the optional mission data areas.
 
 ### Partial Download of ISIS Base Data
 
@@ -331,6 +350,8 @@ This data area contains data that is common between multiple missions such as DE
     cd $ISISDATA
     rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/base .
 
+For versions of ISIS prior to ISIS 4.1.0, please use `isis3data` instead of `isisdata` in the above command.
+
 ### Partial Download of Mission Specific Data
 
 There are many missions supported by ISIS. If you are only working with a few missions then you can save disk space by downloading only those specific data areas. If you want to limit the download even further, read the next section about the SPICE Web Service. Otherwise [jump](#Mission-Specific-Data-Downloads) to the mission specific sections.
@@ -352,6 +373,8 @@ rsync -azv <b>--exclude='kernels'</b> --delete --partial isisdist.astrogeology.u
 
 ### Mission Specific Data Downloads
 
+For versions of ISIS prior to ISIS 4.1.0, please cd into `$ISIS3DATA` instead of `$ISISDATA` and use `isis3data` instead of `isisdata` in all the below rsync commands.
+
 **Apollo Mission:**
 
     cd $ISISDATA