{"action":"created","issue":{"url":"https://api.github.com/repos/TesterTi/LIDCToolbox/issues/8","repository_url":"https://api.github.com/repos/TesterTi/LIDCToolbox","labels_url":"https://api.github.com/repos/TesterTi/LIDCToolbox/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/TesterTi/LIDCToolbox/issues/8/comments","events_url":"https://api.github.com/repos/TesterTi/LIDCToolbox/issues/8/events","html_url":"https://github.com/TesterTi/LIDCToolbox/issues/8","id":384315931,"node_id":"MDU6SXNzdWUzODQzMTU5MzE=","number":8,"title":"Negative pixel values in .dcm images","user":{"login":"stefanknegt","id":17021755,"node_id":"MDQ6VXNlcjE3MDIxNzU1","avatar_url":"https://avatars1.githubusercontent.com/u/17021755?v=4","gravatar_id":"","url":"https://api.github.com/users/stefanknegt","html_url":"https://github.com/stefanknegt","followers_url":"https://api.github.com/users/stefanknegt/followers","following_url":"https://api.github.com/users/stefanknegt/following{/other_user}","gists_url":"https://api.github.com/users/stefanknegt/gists{/gist_id}","starred_url":"https://api.github.com/users/stefanknegt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefanknegt/subscriptions","organizations_url":"https://api.github.com/users/stefanknegt/orgs","repos_url":"https://api.github.com/users/stefanknegt/repos","events_url":"https://api.github.com/users/stefanknegt/events{/privacy}","received_events_url":"https://api.github.com/users/stefanknegt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-11-26T12:49:36Z","updated_at":"2018-11-27T14:33:16Z","closed_at":null,"author_association":"NONE","body":"Related to my previous question, I found out that .dcm files made with Toshiba scanners contain a lot of negative pixel values. Here you can find a histogram of the pixel values for one of the cases in the LIDC dataset.\r\n![toshibaslidebeforepreprocessing](https://user-images.githubusercontent.com/17021755/49014899-dd428700-f181-11e8-8360-62a18efacdeb.png)\r\n\r\nHowever, when I inspect the image that matches this slice after preprocessing it using this toolbox, I see that there are no negative pixel values anymore. And these images are also a lot darker than images from all other scanners. I've inspected the code, but I can only see you replacing the out-of-scan negative pixel values. Could you explain how you deal with negative pixel values in the original dicom images and why they disappear after preprocessing? Thanks a lot!"},"comment":{"url":"https://api.github.com/repos/TesterTi/LIDCToolbox/issues/comments/442079132","html_url":"https://github.com/TesterTi/LIDCToolbox/issues/8#issuecomment-442079132","issue_url":"https://api.github.com/repos/TesterTi/LIDCToolbox/issues/8","id":442079132,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MjA3OTEzMg==","user":{"login":"TesterTi","id":7582117,"node_id":"MDQ6VXNlcjc1ODIxMTc=","avatar_url":"https://avatars0.githubusercontent.com/u/7582117?v=4","gravatar_id":"","url":"https://api.github.com/users/TesterTi","html_url":"https://github.com/TesterTi","followers_url":"https://api.github.com/users/TesterTi/followers","following_url":"https://api.github.com/users/TesterTi/following{/other_user}","gists_url":"https://api.github.com/users/TesterTi/gists{/gist_id}","starred_url":"https://api.github.com/users/TesterTi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TesterTi/subscriptions","organizations_url":"https://api.github.com/users/TesterTi/orgs","repos_url":"https://api.github.com/users/TesterTi/repos","events_url":"https://api.github.com/users/TesterTi/events{/privacy}","received_events_url":"https://api.github.com/users/TesterTi/received_events","type":"User","site_admin":false},"created_at":"2018-11-27T14:33:16Z","updated_at":"2018-11-27T14:33:16Z","author_association":"OWNER","body":"Glad to hear that the above fix works and thanks for pointing out the other issue, it's a rather silly mistake that I had overlooked. It seems that the toolbox is passing the slice spacing to max when it is not needed (i.e. LIDC-IDRI-0599) as I am making the decision to pass it or not on the xml filenames, which are repeated. This is throwing Max's internal calculations off, hence the error. I'm just working on a fix to this which should be committed in an hour or so. The results that are output are correct (max uses the slide spacing to infer correspondences between annotations, but in the toolbox this functionality is not used) but the fix should allow the remaining cases to be output."}}
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