Repository: mne-tools/mne-python

Issue:
documentation and example inconstancy 
https://github.com/mne-tools/mne-python/blob/057026f9a38c63607401ca568790202cf57a08c8/mne/commands/mne_flash_bem.py#L36

According to display documentation, the call should either be 
```
$ mne flash_bem --subject=sample
```
or 
```
$ mne flash_bem -s sample
```

But I could not find the display documentation in the function. Here's the display documentation:
```

Usage: mne flash_bem [options]

Create 3-layer BEM model from Flash MRI images.

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -s SUBJECT, --subject=SUBJECT
                        Subject name
  -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
                        Subjects directory
  -3, --noflash30       Skip the 30-degree flip angle data
  -n, --noconvert       Assume that the Flash MRI images have already been
                        converted to mgz files
  -u, --unwarp          Run grad_unwarp with -unwarp <type> option on each of
                        the converted data sets
  -o, --overwrite       Write over existing .surf files in bem folder
  -v, --view            Show BEM model in 3D for visual inspection

This program assumes that FreeSurfer and MNE are installed and
sourced properly.

This function extracts the BEM surfaces (outer skull, inner skull, and
outer skin) from multiecho FLASH MRI data with spin angles of 5 and 30
degrees. The multiecho FLASH data are inputted in DICOM format.
This function assumes that the Freesurfer segmentation of the subject
has been completed. In particular, the T1.mgz and brain.mgz MRI volumes
should be, as usual, in the subject's mri directory.

Before running this script do the following:
(unless the --noconvert option is specified)

    1. Copy all of your FLASH images in a single directory <source> and
       create a directory <dest> to hold the output of mne_organize_dicom
    2. cd to <dest> and run
       $ mne_organize_dicom <source>
       to create an appropriate directory structure
    3. Create symbolic links to make flash05 and flash30 point to the
       appropriate series:
       $ ln -s <FLASH 5 series dir> flash05
       $ ln -s <FLASH 30 series dir> flash30
       Some partition formats (e.g. FAT32) do not support symbolic links.
       In this case, copy the file to the appropriate series:
       $ cp <FLASH 5 series dir> flash05
       $ cp <FLASH 30 series dir> flash30
    4. cd to the directory where flash05 and flash30 links are
    5. Set SUBJECTS_DIR and SUBJECT environment variables appropriately
    6. Run this script

Example usage:

$ mne flash_bem --subject sample
```


Discussion:
> or
> $ mne flash_bem --s sample

I think this should be `mne flash_bem -s sample`. The Unix standard is single dashes with single letters, double dashes with longer ones. Which is consistent with the docstring:
```
  -s SUBJECT, --subject=SUBJECT
                        Subject name
```
Ahh I see now, you mean in particular the `=` is missing. (My visual `diff` missed this difference.) +1 for updating it, even though in practice I don't think it matters. For example this works:
```
mne browse_raw --raw ~/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif
```
This is either a bug or feature in `optparse` (I'm assuming a feature).
Yes I did a typo while writing the issue. And its either we make it short or we add the `=`, for the example.

not using the `=` was breaking for me. 
@massich can we close or anything to fix?

Resolving patch:
diff --git a/mne/commands/mne_flash_bem.py b/mne/commands/mne_flash_bem.py
--- a/mne/commands/mne_flash_bem.py
+++ b/mne/commands/mne_flash_bem.py
@@ -33,7 +33,7 @@
 
 Example usage:
 
-$ mne flash_bem --subject sample
+$ mne flash_bem --subject=sample
 """
 from __future__ import print_function
 


Test patch: