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syam.gadde
BIAC Staff
USA
421 Posts |
 Posted - Nov 20 2006 : 1:43:51 PM
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| Some of you are using MkFlirtInitMtx.pl, which is a script used to generate an initial matrix to get FSL registration started off on the right foot. This is a script we got from the BIRN. This script is installed in the standard path /usr/local/bin on golgi and so can be called without a full path name. FSL only likes 24 out of the 48 possible orientations; these 24 are the "right-handed"/"radiological" orientations (LAS and all its rotations are acceptable). If it is not in one of these orientations, it will flip the X axis to bring it into an acceptable orientation. If, for example, your data is in LPS, this would trigger a left-right flip. However the version of MkFlirtInitMtx.pl installed since Oct. 16 accounts for this flip when creating the initial matrix, so if you are using this script, be sure you are using the standard one and not one installed in someone's home directory (like mine). |
Edited by - syam.gadde on Nov 20 2006 1:45:09 PM |
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vinod
Average Member
USA
68 Posts |
Posted - Jun 09 2007 : 2:38:28 PM
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| Syam, Do you have any details on what exactly the sctipt does and how it arrives at the values? Is it based on the position of the subject in the scanner or on the functional image bounding box and the actual scanner space? I don't understand why it would be the same for every run of a subject. So, I would appreciate if you can clarify what it does. |
Vinod Venkatraman
IPCN Graduate Student
Huettel Lab
"UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity." - Dennis Ritchie |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jun 09 2007 : 5:35:34 PM
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| The script merely translates the bounding box size and location in scanner space into a form that FSL understands. If you are using the same slice prescription at the scanner for all runs in a study, then this matrix would also be the same across runs. |
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vinod
Average Member
USA
68 Posts |
Posted - Jun 09 2007 : 8:39:19 PM
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| Great. that makes it clear. |
Vinod Venkatraman
IPCN Graduate Student
Huettel Lab
"UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity." - Dennis Ritchie |
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smoski
New Member
16 Posts |
Posted - May 09 2010 : 5:02:54 PM
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I am trying to re-analyze some old data (2006-2007) using scripts of that same vintage. One of them call MkFlirtInitMtx.pl to create the ORIENT.mat file. I get a command not found error when calling this script (running from Meehl) and obviously can't call it on Golgi, as suggested at the beginning of this thread. :-) Where can I find it now?
Thanks! |
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petty
BIAC Staff
USA
453 Posts |
Posted - May 09 2010 : 9:10:19 PM
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| hey moria ,, an old version of the bxh-tools was set as the default on meehl. I updated them, so now the script is in your search path by default. |
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smoski
New Member
16 Posts |
Posted - May 09 2010 : 10:19:45 PM
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| Thanks! |
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Topic |
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passing an initial matrix to FSL
