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petty
BIAC Staff
USA
453 Posts |
 Posted - Dec 09 2005 : 10:03:18 AM
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Here's a short description of the query language syntax: (courtesy of syam)
QUERY: Would match any event where:
CONDITION The CONDITION is true
(QUERY) The QUERY is true
QUERY1 & QUERY2 Both QUERYs are true
QUERY1 | QUERY2 Either QUERY is true
CONDITION: Would match any event where:
param param is > 0
param(>numval) param is greater than numval
param(<numval) param is greater than numval
param(VALUELIST) param equals any value in VALUELIST
param > numval
param >= numval
param < numval
param <= numval
param == numval_or_strval
param != numval_or_strval
[params can be on the right-hand side of these expressions too]
VALUELIST:
VALRANGE
VALRANGE,VALUELIST
VALRANGE: (e.g. "1,3,4-9,22" or "red,green,orange")
strval
numval
numval1-numval2 equivalent to numval1,numval1+1,...,numval2
Definitions:
param any recognized state variable name
strval a string surrounded by quotes (single or double)
numval a number
Examples:
QUERY DESCRIPTION
shape=='square' Match all events whose 'shape' param is 'square'
onset >= 30
Match all events which happened starting at or after time 30
shape=='square' & onset>=30
Match all 'square' events starting at or after time 30
code==4 & color!='red'
Match all events with code 4 whose color is not red
code(2,4,6-10)
Match events whose code is 2,4,6,7,8,9,or 10
actual_response==2
Match events which have a actual_response (perhaps a
button number) param with value 2
actual_response==correct_response
If your events have both the actual_response and
correct_response encoded as parameters, this will
match only correct responses.
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syam.gadde
BIAC Staff
USA
421 Posts |
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petty
BIAC Staff
USA
453 Posts |
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petty
BIAC Staff
USA
453 Posts |
Posted - Dec 16 2005 : 2:23:31 PM
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just a general observation reguarding brain masking.
Because of the 8 channel head coil on the 3T, the default masking routine (if using the option createbrainmask) has a hard time finding the actual brain in spiral images. So i ran a subject through a masked analysis a couple of different ways and i came to the conclusion that the following options worked the best for me:
createbrainmask
brainmaskmethod=threshold
brainmaskthresh=10%
if you put these into your options file, this will change the default from 'localmin', to a thresholded brain mask ... where voxels that exhibit a 10% change from mean are considered to be "brain".
Always make sure you look at your actual --_brainmask.bxh to make sure it looks like a brain, and not a small blob. If it doesn't look like a brain, then you've masked out your actual data. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Apr 28 2006 : 3:35:12 PM
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you can get examples from
/data/users/petty/ES_DEMO |
Edited by - petty on Apr 28 2006 3:40:47 PM |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - May 26 2006 : 11:15:16 AM
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Hello. Do we have job directories for eventstats the way we do for bputil? I'm curious mostly because I've run a lot of eventstats through and I want to clean up any directory that might need it.
Thanks.
Dharol |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - May 26 2006 : 11:26:51 AM
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quote:
Originally posted by tankersley
Hello. Do we have job directories for eventstats the way we do for bputil? I'm curious mostly because I've run a lot of eventstats through and I want to clean up any directory that might need it.
No, it only uses the actual output directory and any temporary files are removed when finished.
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tankersley
BIAC Alum
USA
143 Posts |
Posted - May 29 2006 : 3:31:37 PM
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I successfully ran an entire data set through event stats last week, but now am encountering the following problem:
I type ./eventscreate full_exam#
And this error message appears:
bash: ./eventscreate: The file access permissions do not alow the specified action.
Does anyone know why this would happen and how to fix it?
Thanks,
Dharol
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erin.douglas
BIAC Alum
USA
25 Posts |
Posted - May 29 2006 : 5:11:00 PM
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When I try to run Poker.01 subjects through batchES, Golgi tells me that it cannot find the qa_events*.xml files created by running eventscreate.
In the Golgi command window, I can cd to Poker.01/Data/Func/subject#/QA, and when I ls, the qa_events*.xml are indeed there.
Why is this happening?
Thanks,
Erin |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - May 29 2006 : 5:35:48 PM
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(Dharol) I don't know this program eventscreate, but I guess I know what it does. But without seeing it myself, my guess is that you don't have read permission either to the script eventscreate, or maybe you are not logged in (using cifslogin) to the file server to which it wants to write?
(Erin) As far as batchES is concerned, I might either suspect a typo somewhere or something similar. Find the filename that it is complaining about (I assume it displays the full pathname of a file it can't find) and try an ls on that file and see if the pathname really is correct:
ls FULL_FILENAME |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - May 29 2006 : 6:18:44 PM
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Sitting down with Dharol, the permissions problems were due to opening the script eventscreate in WordPad on Windows, and when it saved it removed executable permission. To restore executable permission to a file, do:
chmod +x MYSCRIPT
However, that was not the only problem. Editing a golgi script in Wordpad is a bad idea, because it will use Windows line-ending characters which are not supported by shells on golgi. Most UNIX systems have programs called dos2unix and unix2dos that will convert the newline conventions from one to the other, but that did not exist on golgi, so I've provided bare-bones versions that you can use:
dos2unix MYFILE
will "fix" any script you may have accidentally edited using WordPad or other Windows editor.
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jun 29 2006 : 09:52:06 AM
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Does anyone know what the following error message means:
Error running /usr/local/bin/bxh_correlate.
Thanks :)
Dharol |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jun 29 2006 : 09:53:31 AM
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When running batches in Eventstats, after the job is finished I get this error message:
Error running /usr/local/bin/bxh_correlate.
Does anyone know what it means?
Thanks :)
Dharol |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jun 29 2006 : 10:06:01 AM
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quote:
Originally posted by tankersley
When running batches in Eventstats, after the job is finished I get this error message:
Error running /usr/local/bin/bxh_correlate.
Does it give any errors before that? In the _LOG.txt file? |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jun 29 2006 : 10:39:58 AM
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Oh -- It's having a problem when it tries to run tcompare. It says:
Number of time points in data and template must match!
Error running /usr/local/bin/bxh_correlate.
My template is:
--template 0,0,0,0.00022185,0.039984446,0.50459248,0.971434037,0.838679245,0.47536268,0.178599023,0.062807994,0 --
It works for running single conditions, so I'm not sure why it doesn't work for the comparison?
Thanks,
Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jun 29 2006 : 10:49:56 AM
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Does it actually run bxh_correlate successfully for some?
bxh_correlate is only run on the individual conditions.
The comparison happens afterwards with bxh_ttest.
What do you specify for ptsbefore and ptsafter?
You have 12 points in your template, so ptsbefore + ptsafter + 1
should equal 12. |
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Topic |
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bxh_eventstats event query language
