Hi to all, I have simulated some PET data using opengate, which is stored in ROOT file and
I want to perform reconstruction with CasToR. But when I type:
$ castor-datafileConversionEx -ih input_file …
It tells me
***** castor-datafileConversionEx :: Unknown option ‘-ih’ !
However, if I just type:
$ castor-datafileConversionEx -ih
(without any file) I get
***** castor-datafileConversionEx :: argument missing for option: -ih
Is parsing in the converter is working correctly?
Hi Fedor,
Why do you use castor-datafileConversionEx instead of castor-GATERootToCastor?
castor-datafileConversionEx is an example code providing guidance regarding how to generate a PET CASToR datafile from any system datafile. It does NOT perform any conversion by itself and must be adjusted to the conversion of any system dataset, dixit help.
Claude COMTAT
BioMaps
Service Hospitalier Frédéric Joliot
91401 Orsay, France
www.biomaps.universite-paris-saclay.fr
Claude COMTAT
BioMaps
Service Hospitalier Frédéric Joliot
91401 Orsay, France
www.biomaps.universite-paris-saclay.fr
Hi Claude,
Thanks. I was not attentive in the documentation.
I am currently at workshop for OpenGate 10 and
now instead of macros they use python code directly. But there is an option in new python library to dump JSON file that has all information that .mac previously had. I think that it is worth to add
to castor new converter which can use JSON instead of .mac.
P. S. However, maybe still parsing in that function should be checked, since the input file is completely unrecognized.
Dear Fedor,
The data structure in root file for Gate 9.X and Gate 10 is different, thus, the standard conversion with Castor tools will not work on Gate 10 output files.
Cheers,
Olga
Moreover, in Gate 10 there is no coincidence sorter yet.
How do you construct your coincidecnes ?
Hi, you are right. What I did is that I just took some toy examples from David Sarrut for simulating PET with Gate 10 in Python. It generated root file, but I am sure that no coincedence sorter is implemented there. Thanks for remark, I guess currently it is no chance to use simulations with Gate 10 in Castor.
Indeed
But you still can use 9.3 version 
Don’t hesitate to ask if you need help
Olga KOCHEBINA
PhD, Ingénieure-chercheuse
Laboratoire d’imagerie BioMedicale
Développements méthodologiques et instrumentaux
Bâtiment: Frédéric Joliot Campus: Orsay - Service hospitalier Frédéric Joliot - 4, Place du Général Leclerc
91401 Orsay
+33 1 69 86 77 39
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