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open-discussion > Orientation issues
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Jul 24, 2012 02:07 PM | Juan Eugenio Iglesias
Orientation issues
ROBEX requires the input to be in the same orientation as the
provided reference volume atlas.img in the directory ref_vols.
Otherwise the registration will fail and the output will be
completely off.
/Eugenio
/Eugenio
Nov 14, 2013 04:11 PM | Juan Eugenio Iglesias
RE: Orientation issues
Not anymore! The new version is based on ITK4 and handles
orientation properly, as long as you have a format that stores
(orientation) header information correctly - for instance Nifti, as
opposed to Analyze. Now, if your image is properly oriented in
World coordinates, ROBEX should process it correctly.
You can test whether your volume is correctly oriented by opening it with a viewer that uses World coordinates (e.g., Freeview in the Freesurfer package) and checking that it is shown in the same orientation as ROBEX/ref_vols/atlas.nii.gz when opened in the same viewer.
You can test whether your volume is correctly oriented by opening it with a viewer that uses World coordinates (e.g., Freeview in the Freesurfer package) and checking that it is shown in the same orientation as ROBEX/ref_vols/atlas.nii.gz when opened in the same viewer.
Nov 21, 2013 03:11 PM | wok
RE: Orientation issues
Thanks, it looks like ROBEX is working fine now. I have tried the
program with the atlas given with the program and with one image of
the IXI database, and the results look fine.
However, had I known the program would be updated this November, I would have banged my head against the wall a lot less with version 1.1, which for some reason would never find that the input image was correctly oriented, no matter my efforts.
However, had I known the program would be updated this November, I would have banged my head against the wall a lot less with version 1.1, which for some reason would never find that the input image was correctly oriented, no matter my efforts.
Nov 21, 2013 04:11 PM | Juan Eugenio Iglesias
RE: Orientation issues
Sorry to hear about your frustrations, NC. I should have done this
much earlier...
In the previous version, the header information of the atlas was incorrect / incomplete due to the use of Analyze, which made it sometimes a nightmare to process the data.
In the previous version, the header information of the atlas was incorrect / incomplete due to the use of Analyze, which made it sometimes a nightmare to process the data.
Nov 21, 2013 07:11 PM | wok
RE: Orientation issues
Do not worry, it has been a bit frustrating for me, but I am now
glad ROBEX is working fine. :)
Although unrelated, I would like to mention I did change the #define for the (hard-coded) paths to the reference volumes so that I could call the program from anywhere on my computer. Otherwise I had to copy the images to the program folder, which was a pain in the end. Thanks for making the code clear and open-source so that these changes are easy to make!
Although unrelated, I would like to mention I did change the #define for the (hard-coded) paths to the reference volumes so that I could call the program from anywhere on my computer. Otherwise I had to copy the images to the program folder, which was a pain in the end. Thanks for making the code clear and open-source so that these changes are easy to make!
Nov 21, 2013 07:11 PM | Juan Eugenio Iglesias
RE: Orientation issues
Since last version, that shouldn't be necessary; you just need to
call robex from the script runROBEX.sh / runROBEX.bat
(Linux/Windows) ;-)