Hi Diana
I've put it here.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/stats2table_alpha.tar.gz
To install
cp stats2table_alpha.tar.gz $FREESURFER_HOME/bin/
cd $FREESURFER_HOME/bin
tar zvxf stats2table_alpha.tar.gz
The binary is named "aparcstats2table_re" ( _re for rewrite which will
be changed to aparcstats2table during the release ) and it will also
install a directory called fsutils/ which contains a few Python helper
scripts.
To view the usage, just type
aparcstats2table_re -h
which should give you an overview of options. There are a few changes
( that means your old aparcstats2table command line *may not* work
fine ) as well as a few feature additions.
* changes - the subject specification is now the same if you use -s
and --subjects ( in accordance with GNU style )
For example, in the prev version, to specify multiple subjects you
could give
aparcstats2table -s sub1 -s sub2
That option is no longer valid. The only way to specify subjects is
aparcstats2table_re --subjects sub1 sub2 ( or )
aparcstats2table_re -s sub1 sub2
the extra features:
* The ROI bug is no longer there. The default behaviour is it finds
the union of all ROIs and displays 0.0 to the ROIs which are not
present in that particular subject.
This behavior can be altered with the "--common-parcs" switch which
only outputs the common ROIs to all the subjects.
To illustrate,
Suppose out of subjects 004, 007, 011... only 004 and 007 have
"unknown" and all 3 have "caudate". The default behavior now is
lh.aparc.meas caudate unknown
004 3.4 4.3
007 2.8 6.7
011 1.3 0.0
Using common-parcs, we get
lh.aparc.meas caudate
004 3.4
007 2.8
011 1.3
* there is an option --report-rois which gives information as to
- what ROIs current subject has and no other subject has and
- what ROI current subject is missing which at-least one other subject
has
The display is still raw and needs work.
* --transpose option switches the order. Usually the subjects are in
the rows and ROIs in the columns. This option transposes. ( looks good
for display )
* --delimiter <tab> ( or <comma> or <semicolon> or <space> ) .. The
delimiter between the measures in the table file.
You can let me know in case of any errors
Krish
On Feb 5, 2009, at 11:29 AM, Douglas N Greve wrote:
Krish actually has a new version and is looking for alpha
testers .... Krish, do you want to give Diana a copy?
doug
Diana Wotruba wrote:
Dear experts
If some of the subjects in a group have missing values of a certain
label, aparcstats2table fails to designate a 0 for them. According
to the freesurfers website, this bug will be fixed in the next
release. Is it already known when this can be expected?
Thanks in advance
Diana
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