Issue added footnote about using CLI from within a repo clone
@@ -6,7 +6,7 @@ Please see the `README.md` in each folder of this [directory](./demos) for more
##### (b) To run an application
-For example, to run a segmentation network:
+For example, to run a segmentation network*:
``` sh
# training
net_segment train -c /path/to/customised_config
@@ -20,6 +20,10 @@ net_segment -h
please see [configuration](../config) documentations for more details and
config file examples.
+ <sup>*Please note that these instructions are for a `pip`-installed NiftyNet.
+If you are using the NiftyNet command line interface from within the NiftyNet source code, please use `python net_segment.py [...]` (provided that the current working directory is the root folder of the NiftyNet repository clone) instead of `net_segment [...]`.
+</sup>
+
Commandline parameters override the default settings defined in `/path/to/customised_config`.
For example,
``` sh
