questions > Automatic stacking for 4D images from UIH
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Apr 5, 2023 05:04 PM | Xicheng Sheng
Automatic stacking for 4D images from UIH
Dear all,
First of all thanks for your tool and the great support you are giving here!
Please excuse my rather basic question:
I am trying to convert some UIH CMRs in dicom to Nifti, using dcm2niix. For a typical folder, there are a total of 225 dcms from time series of 9 slices (00000001.dcm to 00000025.dcm from slice 1, 00000026.dcm to 00000050.dcm from slice 2, and so on). I check that the position tag(0020,0032) is correct, but I cannot get the desired result no matter how -m is set.
The shape of the output file is 336*336*9*25 as expected, but the last two dimensions(slice and time) mix up. Specifically, it seems that time series for the first slice make up [x,y,:,0:2] and [x, y, 0:7, 2] (2*9+7 =25), while ideally it should be [x, y, 0, : ].
Also, here are the info and warnings I got during the conversion:
- DICOM images may be missing, expected 225 spatial locations per volume, but found 9.
- Images sorted by instance number [0020, 0013](1...225), but AcquisitionTime[0008, 0032] suggests a different order(220410.220032)
- Siemens MoCo? Bogus slice timing(range -1,...-1,TR= 2.292 seconds)
- Unable to determine slice direction: please check whether slices are flipped
I wonder whether I can get the correct 4D nifiti file (x,y,z,t) directly from dcmniix.
Thanks in advance.
All the best,
Helen
First of all thanks for your tool and the great support you are giving here!
Please excuse my rather basic question:
I am trying to convert some UIH CMRs in dicom to Nifti, using dcm2niix. For a typical folder, there are a total of 225 dcms from time series of 9 slices (00000001.dcm to 00000025.dcm from slice 1, 00000026.dcm to 00000050.dcm from slice 2, and so on). I check that the position tag(0020,0032) is correct, but I cannot get the desired result no matter how -m is set.
The shape of the output file is 336*336*9*25 as expected, but the last two dimensions(slice and time) mix up. Specifically, it seems that time series for the first slice make up [x,y,:,0:2] and [x, y, 0:7, 2] (2*9+7 =25), while ideally it should be [x, y, 0, : ].
Also, here are the info and warnings I got during the conversion:
- DICOM images may be missing, expected 225 spatial locations per volume, but found 9.
- Images sorted by instance number [0020, 0013](1...225), but AcquisitionTime[0008, 0032] suggests a different order(220410.220032)
- Siemens MoCo? Bogus slice timing(range -1,...-1,TR= 2.292 seconds)
- Unable to determine slice direction: please check whether slices are flipped
I wonder whether I can get the correct 4D nifiti file (x,y,z,t) directly from dcmniix.
Thanks in advance.
All the best,
Helen
Apr 5, 2023 08:04 PM | Chris Rorden
RE: Automatic stacking for 4D images from UIH
I have very little experience with UIH data, and have never seen
fMRI from this manufacturer:
1. Are you using the latest release (v1.0.20220720)?
2. Does the development branch fix your issue? You can get this by selecting your Operating system (win/linux/mac)and downloading the artifact
https://ci.appveyor.com/project/neurolabusc/dcm2niix
3. If these fail, can you send a sample dataset to my institutional email?
https://sc.edu/study/colleges_schools/ar...
1. Are you using the latest release (v1.0.20220720)?
2. Does the development branch fix your issue? You can get this by selecting your Operating system (win/linux/mac)and downloading the artifact
https://ci.appveyor.com/project/neurolabusc/dcm2niix
3. If these fail, can you send a sample dataset to my institutional email?
https://sc.edu/study/colleges_schools/ar...
Apr 6, 2023 03:04 AM | Xicheng Sheng
RE: Automatic stacking for 4D images from UIH
Dear Chris,
Thanks for your prompt reply.
I am with the latest release on MacOS, and the development branch fails either. Unfortunately, I could not share the data for now.
The same problem occurs in a similar dataset CINE_segmented_SAX_InlineVF from Siemens Prisma. I wonder if volumes(z-axis) are stacked first by default, while time series for a slice comes together in my data. Is there any way to force the stacking order with dcm2niix?
Thanks for the help!
Best regards,
Helen
Thanks for your prompt reply.
I am with the latest release on MacOS, and the development branch fails either. Unfortunately, I could not share the data for now.
The same problem occurs in a similar dataset CINE_segmented_SAX_InlineVF from Siemens Prisma. I wonder if volumes(z-axis) are stacked first by default, while time series for a slice comes together in my data. Is there any way to force the stacking order with dcm2niix?
Thanks for the help!
Best regards,
Helen
Apr 6, 2023 10:04 AM | Chris Rorden
RE: Automatic stacking for 4D images from UIH
I can not replicate your issue with UIH data
https://github.com/neurolabusc/dcm_qa_uih
likewise, dcm2niix handles many Siemens datasets as seen in various dcm_qa_* validation datasets as well as usage by many teams. As I can not replicate this issue, I can not provide any insight. However, I do wonder if this issue is not with your raw data, but with corruption caused by a PACS that touched the data or some anonymization tool. I would check the provenance of your data and see if the same issue exists for data exported directly off the scanner without being touched by another tool. If the problem still persists, I suggest working with the Siemens Research Collaboration Managar associated with your center (and the equivalent UIH employee).
https://github.com/neurolabusc/dcm_qa_uih
likewise, dcm2niix handles many Siemens datasets as seen in various dcm_qa_* validation datasets as well as usage by many teams. As I can not replicate this issue, I can not provide any insight. However, I do wonder if this issue is not with your raw data, but with corruption caused by a PACS that touched the data or some anonymization tool. I would check the provenance of your data and see if the same issue exists for data exported directly off the scanner without being touched by another tool. If the problem still persists, I suggest working with the Siemens Research Collaboration Managar associated with your center (and the equivalent UIH employee).
Apr 6, 2023 11:04 AM | Xicheng Sheng
RE: Automatic stacking for 4D images from UIH
Dear Chris,
Thanks for the help and advice.
I would check with our collaborators, and might update you later when we figured it out.
For emergency use, we now simply reorder the array and the headers seem okay.
Thanks again for the tool and help!
Best,
Helen
Thanks for the help and advice.
I would check with our collaborators, and might update you later when we figured it out.
For emergency use, we now simply reorder the array and the headers seem okay.
Thanks again for the tool and help!
Best,
Helen