Request help on DICOM-DSO generated from ePAD

[glhfgg1024]

Hi there, I'm working on this dataset (https://wiki.cancerimagingarchive.net/display/Public/NSCLC+Radiogenomics#503bc643604b462c9c265ca245444274). There are several cases whose segmentation were generated from ePAD and were exported into DICOM DSO format. Then when I was trying to import them into the Slicer, it seems the corresponding CT and the DICOM DSO files have inconsistency alignment. Thus how to get the alignment results? Maybe the CT and the DICOM DSO have different orientations. Thanks a lot! Any comments were greatly appreciated!

[emelalkim]

Hi, I checked the dataset and couldn't find epad generated DSOs. AIMs are all geometric (2D) annotations and in Dicoms Images there are only Slicer segmentations on patients with name starting with R. Can you please point me to a specific one so that I can troubleshoot? Thanks, Emel 2018-03-18 23:37 GMT-07:00 glhfgg1024 <notifications@github.com>:

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Hi there, I'm working on this dataset (https://wiki. cancerimagingarchive.net/display/Public/NSCLC+Radiogenomics# 503bc643604b462c9c265ca245444274). There are several cases whose segmentation were generated from ePAD and were exported into DICOM DSO format. Then when I was trying to import them into the Slicer, it seems the corresponding CT and the DICOM DSO files have inconsistency alignment. Thus how to get the alignment results? Maybe the CT and the DICOM DSO have different orientations. Thanks a lot! Any comments were greatly appreciated! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#51>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AC8LzkQWQ__if3-Li2jVujSKhea1uJG7ks5tf1JCgaJpZM4SvqEf> .

[glhfgg1024]

Hi @emelalkim , thanks a lot for your kind reply and check!

I loaded the following cases named AMC-004 (with ePAD-DSO SEG) and R01-003 (with Slicer SEG).
After loading into the Slicer, the results are as follows:

1. The following three pictures are for AMC-004:

2. The following two pictures are for R01-003:

It seems the R01-003 has the correct segmentation but the AMC-004 doesn't have. And the AMC-004 has three ePAD segmentation.

Maybe I have wrongly loaded the images. If you are convenient, could you please help have a check? Thanks a lot!

[emelalkim]

Hi again, I downloaded the case and troubleshooted. I think these DSOs were created a long while back. The series date is 1997 which it is not possible. About a year and a half ago I fixed these interoperability issues, so I know they were created before that. I tried uploading one to epad and editing it. I just put a dot inside the segmentation to trigger the save. Downloaded the updated DSO and tested it in Slicer. It fixes the issue. See the screenshot below. I'll contact with TCIA people to figure out who submitted these files and more importantly on ways to fix these cases. You are welcome to try opening them in epad and editing like I did meanwhile. Sorry for the inconvenience. Thanks, Emel ​ 2018-03-19 13:41 GMT-07:00 glhfgg1024 <notifications@github.com>:

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Hi @emelalkim <https://github.com/emelalkim> , thanks a lot for your kind reply and check! I loaded the following cases named AMC-004 (with ePAD-DSO SEG) and R01-003 (with Slicer SEG). After loading into the Slicer, the results are as follows: *1. The following two pictures are for AMC-004:* [image: amc-004] <https://user-images.githubusercontent.com/30264480/37620821-54bfb054-2b8b-11e8-9cda-b809057ff2e0.PNG> [image: dso-seg_li] <https://user-images.githubusercontent.com/30264480/37620846-5faa2fd0-2b8b-11e8-8fac-f542c9cfa7c3.jpg> *2. The following two pictures are for R01-003:* [image: r01-003] <https://user-images.githubusercontent.com/30264480/37620854-67349a92-2b8b-11e8-9ed5-7a03cb51d602.PNG> [image: slicer-seg] <https://user-images.githubusercontent.com/30264480/37620856-69c3a172-2b8b-11e8-867a-30da76de5e49.PNG> It seems the R01-003 has the correct segmentation but the AMC-004 doesn't have. And the AMC-004 has three ePAD segmentation. Maybe I have wrongly loaded the images. If you are convenient, please help have a check. Thanks a lot! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#51 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AC8LzrpiIBWjmprdcA5nN8MSFPJ1ulITks5tgBfkgaJpZM4SvqEf> .

[glhfgg1024]

Hi @emelalkim, I'm greatly appreciated for your kind assistance on this!

I've installed the ePAD using docker, but I'm not sure how to connect the downloaded files with AIM onto the ePAD server. Currently I'm not sure how you operated to fix the issue. I'll try that.

I've checked the whole data sets. The following patients have the ePAD-generated DSO segmentation (about 49 cases).

./AMC-004/12-25-1992-CT THORAX-53874/1000-ePAD Generated DSO-82357
./R01-098/11-16-1994-CT Chest Reference Only-12018/1000-ePAD Generated DSO-10657
./R01-099/12-20-1994-CT Chest Reference Only-19320/1000-ePAD Generated DSO-86387
./R01-100/01-04-1995-CT Thorax-39551/1000-ePAD Generated DSO-02648
./R01-101/02-27-1995-ThoraxCHESTWCONTRAST Adult-37779/1000-ePAD Generated DSO-74358
./R01-102/02-13-1995-CT Thorax-85077/1000-ePAD Generated DSO-70883
./R01-103/03-24-1995-CT Thorax-40392/1000-ePAD Generated DSO-07799
./R01-104/04-12-1995-CT Thorax-09030/1000-ePAD Generated DSO-18556
./R01-105/01-26-1995-CT Chest Abd Pelvis Reference Only-32718/1000-ePAD Generated DSO-49726
./R01-106/06-08-1994-CT Chest Reference Only-25536/1000-ePAD Generated DSO-00476
./R01-107/02-24-1995-CT Thorax-62914/1000-ePAD Generated DSO-71768
./R01-108/05-18-1994-CT CHEST WO CONT-DESC-88672/1000-ePAD Generated DSO-83100
./R01-109/07-30-1994-CT CHEST WO CONT-DESC-14996/1000-ePAD Generated DSO-97450
./R01-110/08-02-1994-CT CHEST WO CONT-DESC-81190/1000-ePAD Generated DSO-35055
./R01-111/03-08-1995-CT CHEST WCONT-13988/1000-ePAD Generated DSO-86786
./R01-112/02-27-1995-CT CHEST W CON-86436/1000-ePAD Generated DSO-71090
./R01-113/04-06-1995-CT CHEST WO CONT-52576/1000-ePAD Generated DSO-03752
./R01-114/03-15-1995-CT CHEST WCONT-29806/1000-ePAD Generated DSO-21443
./R01-115/05-04-1995-CT THORAX WO DYE-18972/1000-ePAD Generated DSO-65327
./R01-116/03-22-1995-CT THORAX WDYE-99090/1000-ePAD Generated DSO-88542
./R01-117/03-22-1995-CT CHEST WCON-69240/1000-ePAD Generated DSO-93101
./R01-118/06-14-1995-CT CHEST WO CONTRAST-82801/1000-ePAD Generated DSO-93776
./R01-119/06-28-1995-CT CHEST W-26641/1000-ePAD Generated DSO-81454
./R01-120/09-26-1995-CT CHEST NON CON-73499/1000-ePAD Generated DSO-13339
./R01-121/10-20-1995-CT CHEST W CON-40097/1000-ePAD Generated DSO-56438
./R01-122/09-08-1995-CT CHEST W CON-03755/1000-ePAD Generated DSO-34860
./R01-123/08-17-1995-CT CHEST NON CON-63090/1000-ePAD Generated DSO-88180
./R01-124/11-22-1995-CT CHEST WO-97351/1000-ePAD Generated DSO-72265
./R01-125/07-07-1995-CT Thorax-61175/1000-ePAD Generated DSO-77510
./R01-126/06-21-1995-CT Thorax-58601/1000-ePAD Generated DSO-87407
./R01-127/07-29-1995-Thorax01ROUTINECHEST Adult-30347/1000-ePAD Generated DSO-86726
./R01-128/08-12-1995-CT Chest Reference Only-11585/1000-ePAD Generated DSO-51514
./R01-129/10-17-1995-CT Thorax with Contras-62790/1000-ePAD Generated DSO-32959
./R01-130/09-23-1995-CT Chest Reference Only-63485/1000-ePAD Generated DSO-90224
./R01-131/11-08-1995-CT Thorax-80468/1000-ePAD Generated DSO-49371
./R01-132/10-25-1995-CT Chest Reference Only-23592/1000-ePAD Generated DSO-35150
./R01-133/10-31-1995-ThoraxCHESTCONTRAST Adult-60655/1000-ePAD Generated DSO-98040
./R01-134/12-19-1995-CT Thorax-37750/1000-ePAD Generated DSO-64608
./R01-135/01-17-1996-CT Thorax with Contrast-88591/1000-ePAD Generated DSO-42901
./R01-136/11-21-1995-CT Chest Reference Only-06708/1000-ePAD Generated DSO-02580
./R01-137/01-11-1996-Thorax01ROUTINECHEST Adult-10285/1000-ePAD Generated DSO-84550
./R01-138/12-05-1995-Thorax01ROUTINECHEST Adult-55691/1000-ePAD Generated DSO-25794
./R01-139/03-29-1996-CT Thorax with Contrast-18314/1000-ePAD Generated DSO-93120
./R01-140/04-27-1996-CT Thorax-94030/1000-ePAD Generated DSO-72624
./R01-141/02-27-1996-CT Chest Abdomen and P-49117/1000-ePAD Generated DSO-76954
./R01-142/05-23-1996-CT Chest Reference Only-42721/1000-ePAD Generated DSO-83337
./R01-144/06-26-1996-CT Thorax-50428/1000-ePAD Generated DSO-58685
./R01-145/09-11-1996-ThoraxCHESTCONTRAST Adult-45122/1000-ePAD Generated DSO-44854
./R01-146/08-28-1996-CT Chest Reference Only-27444/1000-ePAD Generated DSO-03566

And about 96 cases have Slicer-generated SEG segmentation. But it seems the remaining 211-96-49=66 cases don't have corresponding segmentation.

Thanks a lot!

[glhfgg1024]

Hi, @emelalkim , I've installed the ePAD web. But I'm not sure how to do next. I cannot upload the selected files. If convenient, could you please give some advice? Thank you!

[emelalkim]

Hi, Just upload all dcm files. You are using the correct interface. You don't need to create the patient and study I assume you are doing. It should analyze all and create the studies and dso annotations. Doesn't it? Does it give an error message? Emel 2018-03-21 19:38 GMT-07:00 glhfgg1024 <notifications@github.com>:

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Hi, @emelalkim <https://github.com/emelalkim> , I've installed the ePAD web. But I'm not sure how to do next. I cannot upload the selected files. If convenient, could you please give some advice? Thank you! [image: test] <https://user-images.githubusercontent.com/30264480/37748061-3cdae424-2d50-11e8-882c-e49aba865ea6.PNG> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#51 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AC8Lztc5bNnAD80Nsyl7ASY0VFP1NzhAks5tgw66gaJpZM4SvqEf> .

[glhfgg1024]

Hi @emelalkim, thanks for your kind check!

I've recorded one short screen video for the importing.

The ePAD server seems running well, but I cannot uploaded the files.

[emelalkim]

hi, it gives an error message saying that it cannot connect to the dcm4che which is the image container. That is why it is not working. When you docker-start epad, it tells you the url to connect. Is master2 correct? Also can you send me the proxy-config.properties file in DicomProxy/etc/ to ealkim@stanford.edu? Feel free to delete any passwords you have changed. Thanks, 2018-03-22 6:52 GMT-07:00 glhfgg1024 <notifications@github.com>:

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Hi @emelalkim <https://github.com/emelalkim>, thanks for your kind check! I've recorded one short screen video for the importing. [image: test ePAD video] <https://www.youtube.com/watch?v=qrRo_Wx77ec> The ePAD server seems running well, but I cannot uploaded the files. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#51 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AC8LztFWymPHA2drDyTcqNVsFr-6-fQjks5tg6yUgaJpZM4SvqEf> .

[Lumemgyi]

@emelalkim Hi!I have read your conversation, and now I am starting to do research on this data set
(https://wiki.cancerimagingarchive.net/display/public/NSCLC+radiogenomics # 503bc643604b 462c9c265ca24544274). However, unlike glhfgg1024, what I do is about pet/ct images in this dataset. I want to know where to download the ROI segmentation image sequence corresponding to the original image or whether it can be converted into ROI segmentation image sequence through xml annotation file. I would appreciate it if you could give me a reply.