AjayLimaye
commented
4 years ago Hi Kyle, You would be able to save image stack from DrishtiImport. Use "Save Images" option to save the stack. Unfortunately DICOM export is not implemented. Cheers, Ajay
On Wed, Aug 7, 2019 at 3:16 PM Kyle Drover notifications@github.com wrote:
Hi Ajay,
Is there anyway to slice processed volumes (pvl.nc files) into .dcm files?
I have microCT scans of embryos (DICOM directories) that have the stage/sample bed in the raw data.
I want to use the Pydpiper package ( https://github.com/Mouse-Imaging-Centre/pydpiper) to automatically identify volume differences between different microCT scans but it requires:
- the sample bed to be removed from these scans.
- These files to be in MINC (.mnc) format.
Currently, I'm using Drishti's --> Data Ops --> Reslice to remove the stage from the volume and then DrishtiPaint to slice the image in .png files (all default settings/parameters). From there, I can create a .tiff stack using FIJI (https://fiji.sc/), change the file extension to .tiff and then use C3D toolkit within a linux virtual machine (https://github.com/CobraLab/MINC-VM) to convert the image into .mnc. These files become unreadable, however, when they are run through the Pydpiper software.
If I can directly save processed volumes as DICOM images, I can just use dcm2mnc (http://bic-mni.github.io/man-pages/man/dcm2mnc.html) to convert these files into .mnc files and ensure that the conversion is not changing the resolution when I'm doing the analysis.
Kind Regards and thank you for reading this Kyle Drover (PhD candidate - Arkell group)
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Ajay Limaye
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dorkylever
Hi Ajay,
Is there anyway to slice processed volumes (pvl.nc files) into .dcm files?
I have microCT scans of embryos (DICOM directories) that have the stage/sample bed in the raw data.
I want to use the Pydpiper package (https://github.com/Mouse-Imaging-Centre/pydpiper) to automatically identify volume differences between different microCT scans but it requires: 1) the sample bed to be removed from these scans. 2) These files to be in MINC (.mnc) format.
Currently, I'm using Drishti's --> Data Ops --> Reslice to remove the stage from the volume and then DrishtiPaint to slice the image in .png files (all default settings/parameters). From there, I can create a .tiff stack using FIJI (https://fiji.sc/), change the file extension to .tiff and then use C3D toolkit within a linux virtual machine (https://github.com/CobraLab/MINC-VM) to convert the image into .mnc.
These files become unreadable, however, when they are run through the Pydpiper software.
If I can directly save processed volumes as DICOM images, I can just use dcm2mnc (http://bic-mni.github.io/man-pages/man/dcm2mnc.html) to convert these files into .mnc files and ensure that the conversion is not changing the resolution when I'm doing the analysis.
Kind Regards and thank you for reading this Kyle Drover (PhD candidate - Arkell group)