users > Trouble with reformatting
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Sep 16, 2010 04:09 PM | Rob Campbell
Trouble with reformatting
Hi,
I am trying to use munger.pl to coordinate image registration. I am stating off with the example data from the Stanford site. Everything seems to go well on a Mac but I'm having problems under Linux. Although I supply the "-r 01" flag, which requests for the image to be re-formatted using the calculated parameters, no re-formatting is taking place. It does, however, calculate the registration parameters.
At the start of the registration I see a warning message:
WARNING: image does not have valid orientation meta information; cannot reorient.
Could this be the reason? Oddly, I don't see this message on the Mac even through I am using the same example data. This led me to think that the meta information truly is absent but that the Mac build of registration doesn't report this. Any ideas?
Thanks
I am trying to use munger.pl to coordinate image registration. I am stating off with the example data from the Stanford site. Everything seems to go well on a Mac but I'm having problems under Linux. Although I supply the "-r 01" flag, which requests for the image to be re-formatted using the calculated parameters, no re-formatting is taking place. It does, however, calculate the registration parameters.
At the start of the registration I see a warning message:
WARNING: image does not have valid orientation meta information; cannot reorient.
Could this be the reason? Oddly, I don't see this message on the Mac even through I am using the same example data. This led me to think that the meta information truly is absent but that the Mac build of registration doesn't report this. Any ideas?
Thanks
Sep 16, 2010 05:09 PM | Torsten Rohlfing
RE: Trouble with reformatting
Hi Rob:
In general, only "medical" images have valid orientation information in terms of CMTK's I/O functions.
Since you are using Greg's script for registration and reformatting, I am going to assume you are working on "biological" data instead.
As a bit of background, CMTK attempts to orient all images it reads such that they are in "RAS" orientation. That is, the registration code can then assume that the fastest moving index in the pixel array goes from patient Left to Right, the second-fastest from Posterior to Anterior, and the third-fastest from Inferior to Superior. The actual storage order of the pixels on disk is typically deduced from fields of the input file format, such as DICOM orientation tags, NIFTI direction cosines or quaternions, etc.
For microscopy data, there aren't usually any such data fields, and even if there were, they aren't usually represented by R/L, A/P, and S/I orientations, because your specimen simply aren't people ;)
All that said, there is no reason why you should get a warning on one platform and not on the other. If the image file doesn't have orientation information, it doesn't on any platform.
Speaking of which - what *is* the image format you are reading?
Second, I cannot see of a reason why the reformat tool shouldn't read and properly use an image that the registration tool can. Both tools are using the exact same I/O functions to read their inputs.
That said, I'd be happy to do some debugging if you could send me (i.e., upload somewhere) the images you are having problems with, preferably together with a transformation file that you said the script does compute.
Best,
Torsten
Originally posted by Rob Campbell:
In general, only "medical" images have valid orientation information in terms of CMTK's I/O functions.
Since you are using Greg's script for registration and reformatting, I am going to assume you are working on "biological" data instead.
As a bit of background, CMTK attempts to orient all images it reads such that they are in "RAS" orientation. That is, the registration code can then assume that the fastest moving index in the pixel array goes from patient Left to Right, the second-fastest from Posterior to Anterior, and the third-fastest from Inferior to Superior. The actual storage order of the pixels on disk is typically deduced from fields of the input file format, such as DICOM orientation tags, NIFTI direction cosines or quaternions, etc.
For microscopy data, there aren't usually any such data fields, and even if there were, they aren't usually represented by R/L, A/P, and S/I orientations, because your specimen simply aren't people ;)
All that said, there is no reason why you should get a warning on one platform and not on the other. If the image file doesn't have orientation information, it doesn't on any platform.
Speaking of which - what *is* the image format you are reading?
Second, I cannot see of a reason why the reformat tool shouldn't read and properly use an image that the registration tool can. Both tools are using the exact same I/O functions to read their inputs.
That said, I'd be happy to do some debugging if you could send me (i.e., upload somewhere) the images you are having problems with, preferably together with a transformation file that you said the script does compute.
Best,
Torsten
Originally posted by Rob Campbell:
Hi,
At the start of the registration I see a warning message:
WARNING: image does not have valid orientation meta information; cannot reorient.
Could this be the reason? Oddly, I don't see this message on the Mac even through I am using the same example data. This led me to think that the meta information truly is absent but that the Mac build of registration doesn't report this. Any ideas?
Thanks[/userquote]
At the start of the registration I see a warning message:
WARNING: image does not have valid orientation meta information; cannot reorient.
Could this be the reason? Oddly, I don't see this message on the Mac even through I am using the same example data. This led me to think that the meta information truly is absent but that the Mac build of registration doesn't report this. Any ideas?
Thanks[/userquote]
Sep 16, 2010 06:09 PM | Greg Jefferis
RE: Trouble with reformatting
The reason the error only appears on linux is that you are using
CMTK binaries downloaded from NITRC on linux and much older
binaries downloaded from flybrain.stanford.edu on mac. Greg.
Sep 17, 2010 04:09 AM | Greg Jefferis
RE: Trouble with reformatting
Torsten has answered the second part of the question. The first
part concerns use of my munger.pl script to coordinate many
registrations. The basic problem is that the registration software
and control scripts available from flybrain.stanford.edu at the
moment (Sep 2010) are still those released in 2007 when CMTK was
closed source. Many changes have happened in the interim. You
should now obviously prefer the CMTK binaries available from this
site. You should also prefer the most up to date version of
munger.pl which lives here:
http://github.com/jefferis/AnalysisSuite...
I hope that the README at the bottom of that page explains things well enough.
http://github.com/jefferis/AnalysisSuite...
I hope that the README at the bottom of that page explains things well enough.
Sep 17, 2010 07:09 AM | Torsten Rohlfing
RE: Trouble with reformatting
Greg:
Just to confirm - in your experience your current script should work properly with the current CMTK tools, correct?
Thanks!
Torsten
Originally posted by Greg Jefferis:
Just to confirm - in your experience your current script should work properly with the current CMTK tools, correct?
Thanks!
Torsten
Originally posted by Greg Jefferis:
Torsten has answered the second part of the
question. The first part concerns use of my munger.pl script to
coordinate many registrations. The basic problem is that the
registration software and control scripts available from
flybrain.stanford.edu at the moment (Sep 2010) are still those
released in 2007 when CMTK was closed source. Many changes have
happened in the interim. You should now obviously prefer the CMTK
binaries available from this site. You should also prefer the most
up to date version of munger.pl which lives here:
http://github.com/jefferis/AnalysisSuite...
I hope that the README at the bottom of that page explains things well enough.[/userquote]
http://github.com/jefferis/AnalysisSuite...
I hope that the README at the bottom of that page explains things well enough.[/userquote]