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Bethany
BIAC Alum

37 Posts
Posted - Jun 27 2007 :  11:50:47 AM  Show Profile  Reply with Quote
I'm having some registration problems in FEAT with RiskTime.02: all my brains are coming out backwards relative to the standard space. The solutions I've read so far are to use the BET brain extraction on the anatomicals (which I'm doing: I didn't know FEAT would run without it) and to use the following command:

MkFlirtInitMtx.pl --in ~/net/goldman/data/BIAC/RiskTime.02/Data/FSL/33231/anat1.bxh --stdref --o
 ~/net/goldman/data/BIAC/RiskTime.02/Data/FSL/33231/ORIENT.mat


to make an orient file and then insert it into the .fsf file and run FEAT from the command line. I've done that, too, but my brains are still backwards.

Is there anything else I should be trying to see if I can get my heads on straight? (Sorry, couldn't resist.)
Edited by - Bethany on Jun 27 2007 11:51:39 AM

syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jun 27 2007 :  12:08:56 PM  Show Profile  Reply with Quote
There could be several reasons why this is happening. But I suspect that your matrix is not being used -- looking at your .fsf file, it just points to ORIENT.mat, but you really need to specify a full pathname, otherwise it won't be able to find it when it is running in the new .feat directory.
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Bethany
BIAC Alum

37 Posts
Posted - Jun 27 2007 :  12:18:13 PM  Show Profile  Reply with Quote
That makes sense. I also had this problem in a test analysis I did on RiskTime.01, which was running from a batch file that should have plugged the full path of the orient file into the fsf file when it ran. However, I'll give it another try and see if giving the path helps. Thanks!
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Bethany
BIAC Alum

37 Posts
Posted - Jun 27 2007 :  2:57:28 PM  Show Profile  Reply with Quote
OK, I'm not totally sure but I think it's the right way 'round now:

\\Goldman\Data\BIAC\RiskTime.02\Data\FSL\33231+++.feat\reg\highres2standard.gif

However, is it just me or is it sort of... tilted?
Edited by - Bethany on Jun 27 2007 3:02:26 PM
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Bethany
BIAC Alum

37 Posts
Posted - Jun 27 2007 :  4:39:48 PM  Show Profile  Reply with Quote
Making the orient file on the first functional instead of the anatomical seems to have fixed the tilting problem, at least for the time being. Thanks for the suggestion!
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syam.gadde
BIAC Staff

USA
421 Posts
Posted - Jun 27 2007 :  4:52:46 PM  Show Profile  Reply with Quote
Glad that worked. Just so there is no confusion, my suggestion was to try omitting the highres image as a intermediary registration and just go straight from functional to standard and see if that helps. Using the highres as an intermediary has not been as reliable as I had expected on some data sets I have run, and I wonder if others at BIAC have had the same experience.
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