[Homer-users] New HOMER release (with a few major fixes)

[thuppert]

Hey all-

    It recently came to my attention that the version of HOMER that we had
on the web as the pcode version for Matlab 6.5 (and possibly 6.1 as well)
was accidently compiled from an older version of the code that had a major
bug in it.  I had fixed the problem, the code was compiled without this
change in it.  The bug resulted in mishandling of complex data sets (such as
those from Cw5) as well as miscalulating dOD and dConc in all data.  A newer
version with this mistake is on the web @
http://www.nmr.mgh.harvard.edu/DOT/resources/homer.htm  (This is also
updated on the internal site in matlab *.m code)

Make sure to update the Matlab Path with when installing this new code.

There are also a few additions/changes to the code:

   The filtering (updating) now applies the low-pass filter to the raw data
rather then the normalized data.  As a result, the "Norm" and "Norm_Cov"
displays have been low-pass filtered already.  Previously, LPF was done
after normalizing.  HPF is still done after "Norm_Cov" but before dOD  (see
user's guide for details)

   A feature called Plot All (under Figures>>Plot All) was added.  This will
plot all the src-det pairs as they appear in the probe.  This is done for
dOD or dConc (and for AvgAll or only current file).  Data must be averaged
first to use this.

   A number of warning messages were added to the imaging menu (and
elsewheres)

   The Advanced options {filtering and imaging) menus were updated to
include such features as display contrast-to-noise image (with noise
calculated as the StdDev (wrt time) of an image created from the filtered
baseline).  For this baseline must be specified and this is currently only
available for dOD (not dConc images).  Also in the filtering menu, partial
volume/pathlength corrections can be specified if desired and there's a
custom filtering option (see User's guide)

	The code was changed to allow more freedom in averaging epochs.  Now only a
single stim point can be specified and the pre-time can be set to zero
(previous versions wanted at least 2 points).  (It can be set to a positive
number as well, but then the data is normalized to the first point- if a
pre-time is specified, the data is normalized to set the mean of the
pre-time to zero)

	There were a few minor syntext errors dealing with older *.mat file from
previous versions of the code that I fixed (That probably doesn't effect
anyone).

	The color pallette was expanded to allow up to 32 channels to be displayed
at once (i.e. if you had one detector that saw all 32 lasers).  [However, I
wouldn;t recomend dealing with data sets that large- Matlab is not the most
efficient program for huge data sets]

	I also fixed the movie features.  I want to put more control over the
compression/frame rate but this will have to wait till a later version.




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For those who didn't get my email last week, I put up a new User's guide as
well describing all the features.

Also, I encorouge everyone to use the  'homer-users at nmr.mgh.harvard.edu'
email server to communicate issues/ comments/ etc.  Hopefully, this change
will fix all the problems that people have been having.

If you have not yet signed up for the HOMEr-users email server and wish to,
you can/should do so off the same site for downloading HOMER.  I'm not going
to include individual names on these emails anymore (so if you don't wanna
be on the list this is my last such email)-  I just wasn't sure everyone was
on the list who wanted to be and got this message.


--Again, I'm sorry about having to essentially recall the program and make
this change- but this is what happens when you sit on the edge of research.

Ted Huppert, MS

PhD student-Harvard Univ.
Dept of Biophysics
Photo Migration Imaging lab
Mass General Hospital/CNY

Tele: (617)726-4020
Cell: (617) 869-1205
thuppert at nmr.mgh.harvard.edu