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
We have done a rewrite of both aparcstats2table and asegstats2table, although it needs a little a bit of testing, still. I'll put the new version online and send you the link soon. It will be great if you can test i) the bug in question and ii) aparcstats2table in general.
Both will definitely be in our next release.
-Krish
On Feb 5, 2009, at 9:24 AM, 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Diana
I have put the latest rewrite ( more fixes and updates ) of both the aparcstats2table and asegstats2table here. If you still haven't tried with the previous one we sent you, use this version instead.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/stats2table.tar.gz
Extract it in your FREESURFER_HOME/bin directory ( this will overwrite the a*stats2table files )
This version honors both the type of inputs for the subjects. For example, you can specify subjects with
-s sub1 -s sub2 ...
as well as
--subjects sub1 sub2 ..
~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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Diana Wotruba -
Douglas N Greve -
Krish Subramaniam