Hi,
Sorry to have started such a discussion ;-) .
I had in mind not to change the existing synatax, but to extend it in a
way, that there is a common set of arguments used throughout the tools.
In some tools this is allready the case. In an early version change
there was much trouble in changing tool names (avw* to fsl*) which was a
nasty effort to get old scripts working. I absolutely do not intend to
suggest making major changes in the syntax that would not allow to use
existing scripts with future versions of fsl. Instead just to have a
common set of arguments throughout all tools might be added, while the
existing ones are kept.
If my comment means that I have to adapt all my scripts in the near
future I would hate myself to have started this thread...
wolf
On 03/02/2010 06:15 PM, Matt Glasser wrote:
> I think the backwards compatibility would be nice, even if it means more
> items in $FSLDIR/bin.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Mark Jenkinson
> Sent: Tuesday, March 02, 2010 9:44 AM
> To: [log in to unmask]
> Subject: Re: [FSL] plead for consistency of arguments
>
> I'm torn here, as I would also like consistency but I also do not
> want to break existing scripts (ours or others) that rely on the
> existing syntax. One way forward is to create new tools which
> wrap previous tools with new syntax. This wouldn't be too hard,
> although it would add to the already high number of names
> in $FSLDIR/bin. What do people generally think about this?
>
> All the best,
> Mark
>
>
> On 2 Mar 2010, at 15:37, Michael Hanke wrote:
>
>
>> On Tue, Mar 02, 2010 at 03:15:14PM +0000, Rolf Heckemann wrote:
>>
>>> I second the pleading. FSL currently does a great job of mimicking
>>> all those inconsistencies in the unix world, but perhaps it would be
>>> nicer for users if it stopped doing that and mimicked, say, GNU tools
>>> instead, which are much more internally consistent.
>>>
>> FSL is a slightly more than 100 lines of code. What you ask for is
>> something that needs a little longer than an afternoon. If you (or
>> anyone else interested in having this changed) have a patch that does
>> the modifications for _all of FSL_ we could test-drive it on a fork of
>> the Debian package.
>>
>> But be aware that you would have to put some manpower into maintaining
>> such patch until it has proven to be fully functional _and_ migrated
>> into FSL proper....
>>
>> Michael
>>
>>
>>
>>
>>> On Tue, Mar 02, 2010 at 02:38:35PM +0000, Stephen Smith wrote:
>>>
>>>> Just like across all Unix tools you mean?
>>>>
>>>> :)
>>>>
>>>> On 2 Mar 2010, at 14:34, wolf zinke wrote:
>>>>
>>>> Hi,
>>>> I am really grateful for the FSL package and the great support.
>>>> Thank
>>>> you so much for providing it for free and also giving such a
>>>> thorough
>>>> support.
>>>> However, nothing can't be perfect and there is always space for
>>>> improvements. One aspect that I encounter pretty often when
>>>> doing some
>>>> scripting is a inconsistency of function arguments between
>>>> different
>>>> tools. I think this is most clear when comparing flirt and fnirt.
>>>> While flirt uses the '-' convention with a space before the next
>>>> argument, fnirt uses '--' with only '=' between the argument.
>>>> Furthermore, some arguments seem to be named differently, eg
>>>> 'nn' and
>>>> 'nearestneighbour' for the interpolation method. I am currently
>>>> writing a small wrapper script that switches between fnirt and
>>>> flirt,
>>>> and I need to build in some ad hoc correction routines that
>>>> translate
>>>> the arguments. It would be great, if such workarounds could be
>>>> avoided
>>>> by using the arguments in a consistent manner between the various
>>>> tools.
>>>> I guess that such inconsistencies are rare and a result of the
>>>> development history, but whenever I encounter them they disturb my
>>>> workflow quiet a bit :'( . So I just wanted to make this
>>>> suggestion.
>>>> Please don't feel offended, since I really do like working with
>>>> the
>>>> FSL tools.
>>>> thanks,
>>>> wolf
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>> -----
>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>> Associate Director, Oxford University FMRIB Centre
>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> +44 (0) 1865 222726 (fax 222717)
>>>> [1][log in to unmask] [2]http://www.fmrib.ox.ac.uk/~steve
>>>>
>>>> ----------------------------------------------------------------------
>>>> -----
>>>>
>>>> References
>>>>
>>>> 1. mailto:[log in to unmask]
>>>> 2. http://www.fmrib.ox.ac.uk/~steve
>>>>
>>> --
>>> Rolf A Heckemann, MD PhD
>>> Médecin chercheur
>>> Fondation Neurodis
>>> CERMEP - Imagerie du Vivant
>>> Hôpital Neurologique Pierre Wertheimer
>>> 59 Boulevard Pinel
>>> 69003 Lyon
>>> France
>>>
>>>
>>> 1267542281
>>>
>>>
>>
>>
>> --
>> GPG key: 1024D/3144BE0F Michael Hanke
>> http://mih.voxindeserto.de
>>
>>
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