| T O P I C R E V I E W |
| syam.gadde |
Posted - Nov 20 2006 : 1:43:51 PM
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). |
| 6 L A T E S T R E P L I E S (Newest First) |
| smoski |
Posted - May 09 2010 : 10:19:45 PM
Thanks! |
| petty |
Posted - May 09 2010 : 9:10:19 PM
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. |
| smoski |
Posted - May 09 2010 : 5:02:54 PM
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! |
| vinod |
Posted - Jun 09 2007 : 8:39:19 PM
Great. that makes it clear. |
| syam.gadde |
Posted - Jun 09 2007 : 5:35:34 PM
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. |
| vinod |
Posted - Jun 09 2007 : 2:38:28 PM
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. |
