@laura_rodriguez is is possible you could share these files for debugging? Or if you want to debug yourself, you could try loading the data into the DICOM database and then going into advanced mode and looking at the metadata. As you scroll through the slices you can look at the ImagePositionPatient and see how it is changing and compare this to the slice spacing shown for the loaded volume in the Volumes module. You could also change the spacing to find out what value matches the Mimics view. Also you could check the error logs for any diagnostic information.
@doc-xie importing through the DICOM module in the current nightly should autocorrect the gantry tilt if the files are like the examples I have here (the ones I posted earlier in this thread). If neither that nor the manual shear technique are working on other data then Iâm not sure what else to suggestâŚ
You can now also filter for tags and copy value of all frames at once. It would help us a lot if you could copy-paste here value of Image Position Patient tag for all frames.
@pieper it looks to be everything ok in medata about the patient positionâŚ
See this one too
You are saying that I can change the paramaters, can you explain me how?
You can view/adjust voxel size in Volumes module: Volume information section, Image Spacing values.
@laura_rodriguez Could you please enter ImagePositionPatient into the Search... box, click Copy all files metadata button (it copies all ImagePositionPatient values to the clipboard), and paste the clipboard content here? We could then double-check that all position values are correct.
It does not me allow to send you the complete file because i have to many filesâŚ
Can I send you in another way? Thank you
L
If you follow my instructions above (enter filter criteria in search box and click copy all files metadata), field values are copied to the clipboard. Then, you can just paste the clipboard content here. There are no files involved.
Neither, this is what the app is telling me:
Body is limited to 36500 characters; you entered 81668.
I see, the info is too long. Then please copy into notepad or word, save the file to dropbox (or onedrive, or google drive) and paste here the link to the file. Thanks!
Thank you. The file shows that distance between all neighbor slices are 0.5mm. What are the 3 Image Spacing values in Volumes module / Volume information section?
Correct values would be 0.35026, 0.35026, 0.5.
@pieper Do you know what could cause seeing 1,1,1 spacing, while the slice position seems to be correct and pixel spacing tag is present?
@laura_rodriguez Could you share the DICOM files and post the link here? (make sure data is anonymized, if belongs to patients)
@lassoan no, Iân not sure why that would be happening but I would like to figure it out. The slice thickness is set to be 1mm, but the spacing is clearly 0.5mm.
@laura_rodriguez it really would help to have a look at the data. If you canât share it publicly with a link on the forum perhaps you could share it privately with me and @lassoan. Also do you know if this data was processed in any way or did it come straight from a scanner?
Hello,Professor Lassoan!
How can you get the values(0.35026,0.35026,0.5) basing the Image Spacing(1mm,1mm,1mm) and what should do in the next in order to correct the images?
Thanks a lot!
Doc-xie
0.35026, 0.35026 values come from Pixel Spacing tag (I could see it in the screenshots).
0.5 is computed from values in Image Position Patient tags (slice position difference between neighbor slices).
If you can share the data set then we can make sure that Slicer loads it correctly.
Ok, it is working now, Changing the values, thank you very much for this. I will continue âplaying with the softwareâ
I cannot share the data with you through here, because they are highly confidential. sorry. I do not have problems in sharing a partial part. if that can work to you
Getting 3-5 neighbor slices would probably be enough (you can choose frames that are almost empty, as for the testing we only need the DICOM tags).