Request help on AIMConverter.exe

[glhfgg1024]

Hi Dear Sir/Madam,

Thanks for sharing this valuable toolkit!
I have a problem, I want to convert the AIM XML files to DICOM-RT file.
I use the following command:

C:\annotation-and-image-markup-master\AIMToolkit_v4.0.0_rv44\source\AIMLib\Release\x64>AIMConverter.exe -i AIM -o SR AMC-003.xml AMC-003

But there are some errors as follows:

Error: Error writing annotation(s) to file "AMC-003":
Annotation Collection Validation Errors:
Annotation Collection Unique Identifier
II value is not a valid UID
UID must constist of digits and periods(.) only

Usage:
AIMConverter.exe -i[nput] AIM|SR|CDA -o[utput] AIM|SR|CDA input_file output_file

If convenient, could you please give some advice? Thanks a lot!

[vkleper]

Hello glhfgg1024, Based on the information you provided and without seeing the input, I can say this: 1. The error you are seeing informs you that one or more values for UID specified in the AIM-003.xml are invalid DICOM UID values. Though misspelled, the error says that UID content validation fails as the UID value has things other that digits and periods. See DICOM PS3.5 Chapter 9 for full UID specification: http://dicom.nema.org/dicom/2013/output/chtml/part05/chapter_9.html 2. Unfortunately, AIMConverter.exe does not create DICOM-RT instances. The tool only converts between AIM XML documents and proprietary AIM DICOM SR instances. Regards, Vlad

…

On Tue, Jan 9, 2018 at 9:26 PM, glhfgg1024 ***@***.***> wrote: Hi Dear Sir/Madam, Thanks for sharing this valuable toolkit! I have a problem, I want to convert the AIM XML files to DICOM-RT file. I use the following command: C:\annotation-and-image-markup-master\AIMToolkit_v4.0.0_rv44\source\AIMLib\Release\x64>AIMConverter.exe -i AIM -o SR AMC-003.xml AMC-003 But there are some errors as follows: Error: Error writing annotation(s) to file "AMC-003": Annotation Collection Validation Errors: Annotation Collection Unique Identifier II value is not a valid UID UID must constist of digits and periods(.) only Usage: AIMConverter.exe -i[nput] AIM|SR|CDA -o[utput] AIM|SR|CDA input_file output_file If convenient, could you please give some advice? Thanks a lot! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD2ibPjKiGlfyL_7x9UlY5QZ2KdtmEg8ks5tJC3TgaJpZM4RYwqk> .

[glhfgg1024]

Hi, @vkleper, thanks a lot for your kind comments and suggestions!

Yeah, after debugging the code, I've found that the UID in AIM-003.xml is as follows:

<uniqueIdentifier root="hnmh13izcz8kr4gxa1efkiaygscgfv77jz79mvoy"></uniqueIdentifier>

But in the header of this xml, it shows:

<ImageAnnotationCollection aimVersion="AIMv4_0" xmlns="gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM AIM_v4_rv44_XML.xsd">

So from the header, it seems the xml is generated from AIM 4.1.0 version. But when I tried to convert the AIM-003.xml to AIM-003.dcm, it would fail.

When I commented the validation code in "ModelValidator.cpp",

bool ModelValidator::isValid(const iso_21090::II& ii, bool allowDefaults /*= false*/)
{
    //RETURN_IF_UID_NOT_VALID(ii.toString(), "II");
    return true;
}

Then other errors occured:

(base) C:\annotation-and-image-markup-master\AIMToolkit_v4.1.0_rv44\source\AIMLib\Release\x64>AIMConverter.exe -i XML -o SR ./AMC-003.xml AMC-003.dcm
Error: Error writing annotation(s) to file "AMC-003.dcm":
Annotation Collection Validation Errors:
Person is invalid
Birth Date is invalid
Month value must be between 1 and 12

So, I'm not sure if the AMC-003.xml was generated from AIM 4.1.0.

[vkleper]

Hi @glhfgg1024, I hope I'm not too late with my reply. As the first test, your may try validating your XML documents against AIM Schema (AIM_v4_rv44_XML.xsd, etc.) using any standard XML validation tool. If the annotations validate, without seeing your complete annotation files, I can only guess that some values are incorrectly represented in them. AIM Schema uses ISO 21090 data types that allow for multiple different value formats in a single type. DICOM requirements are more stringent. Yeah, after debugging the code, I've found that the UID in AIM-003.xml is

as follows: <uniqueIdentifier root="hnmh13izcz8kr4gxa1efkiaygscgfv77jz79mvoy"></uniqueIdentifier>

As I mentioned earlier, the problem is with the way that specific UID was created. While it may be a valid ISO 21090 II data type value, for a DICOM UID to be valid, it has to conform to DICOM PS3.5 Chapter 9 for full UID specification: http://dicom.nema.org/dicom/2013/output/chtml/part05/ chapter_9.html That's what AIMConverter's validator is checking for. Then other errors occured:

(base) C:\annotation-and-image-markup-master\AIMToolkit_v4.1.0_rv44\source\AIMLib\Release\x64>AIMConverter.exe -i XML -o SR ./AMC-003.xml AMC-003.dcm Error: Error writing annotation(s) to file "AMC-003.dcm": Annotation Collection Validation Errors: Person is invalid Birth Date is invalid Month value must be between 1 and 12 Whoever encoded the Birth Date of a patient, didn't provide a correct

value. And if it's empty, empty values are not allowed. So, I'm not sure if the AMC-003.xml was generated from AIM 4.1.0.

You are right. It appears that a tool other than AIMToolkit 4.1.0 was used to generate your annotations. In general, you may still be able to use AIMConverter if your XML annotations pass external AIM XML Schema validation and you are able to correct data errors. One way to fix data errors would be to write a small XML transformation to correct or remove the offending parts of the annotations. Then use the AIMConverter on the cleaned up data.

…

On Thu, Jan 11, 2018 at 8:52 AM, glhfgg1024 ***@***.***> wrote: Hi, @vkleper <https://github.com/vkleper>, thanks a lot for your kind comments and suggestions! Yeah, after debugging the code, I've found that the UID in AIM-003.xml is as follows: <uniqueIdentifier root="hnmh13izcz8kr4gxa1efkiaygscgfv77jz79mvoy"></uniqueIdentifier> But in the header of this xml, it shows: <ImageAnnotationCollection aimVersion="AIMv4_0" xmlns="gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="gme://caCORE.caCORE/4.4/edu.northwestern.radiology.AIM AIM_v4_rv44_XML.xsd"> So from the header, it seems the xml is generated from AIM 4.1.0 version. But when I tried to convert the AIM-003.xml to AIM-003.dcm, it would fail. When I commented the validation code in "ModelValidator.cpp", bool ModelValidator::isValid(const iso_21090::II& ii, bool allowDefaults /*= false*/) { //RETURN_IF_UID_NOT_VALID(ii.toString(), "II"); return true; } Then other errors occured: (base) C:\annotation-and-image-markup-master\AIMToolkit_v4.1.0_rv44\source\AIMLib\Release\x64>AIMConverter.exe -i XML -o SR ./AMC-003.xml AMC-003.dcm Error: Error writing annotation(s) to file "AMC-003.dcm": Annotation Collection Validation Errors: Person is invalid Birth Date is invalid Month value must be between 1 and 12 So, I'm not sure if the AMC-003.xml was generated from AIM 4.1.0. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD2ibAUB7KD-7brxyZTXCDnGqAlD3_cyks5tJiAugaJpZM4RYwqk> .

[glhfgg1024]

Hi @vkleper , thanks a lot for your kind reply and suggestions!

I'm trying to parse https://wiki.cancerimagingarchive.net/download/attachments/28672347/AIM_files.zip?version=1&modificationDate=1512415990689&api=v2 file.

Yeah, I also found that the data creator may use other version of AIMConverter to generate their files.
Thanks a lot for your kind suggestions!

[constiDisch]

Hi @glhfgg1024 ,
I am running into the same problem, when reading the (updated?) data from https://wiki.cancerimagingarchive.net/display/Public/NSCLC+Radiogenomics . Could you give me a hint how you solved the problem?