How to Measure a Brain Tumor As a 3D Volume
Ask a surgeon to request a "3D" protocol for MRI scan., Make sure the RadTech understands what you want., Get CD of Dicom data from Radiologist., Upload contents of CD to Dropbox or Google Drive., Install "ONIS" free DICOM viewer version on PC., Set...
Step-by-Step Guide
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Step 1: Ask a surgeon to request a "3D" protocol for MRI scan.
This is becoming common because surgeons are using image guided surgery software in the OR.
The protocol is 1mm slices, no spacing, 512x512 resolution, contrast injection. -
Step 2: Make sure the RadTech understands what you want.
If you don't get good data, you can't get a 3D volume.
This will probably be an Axial 3D SPGR 1mm no spacing if you instructed the radtech to do it.
It is best to get a 3D scan in all three planes, Axial, Sagital and Coronal.
The Radiologist doesn't know how to operated the MRI machine or software so you need to instruct the RadTech what you want.
Radiologist like to "reformat" a scan.
This doesn't give good 3D data for sequencing.
You can also ask to scan only the region of the tumor.
This is a new function on GE scanners and most Rad Techs know what to do, but the radiologists are lost because this wasn't a function they had in the film days of past.
They are used to looking at the entire head, instead of just the region where the tumor is. , This should be the easy part, but the Radtech can't bill for this and the front office girls aren't computer literate, so it ends up being difficult.
They are required to do it now, so insist.
Radiologists are very protective of their data.
The good thing, is it isn't their data, it is yours. , Having it on the cloud will allow you to access it from any device. , They don't have a MAC version yet.
Most Radiologists are giving a free version of a viewer on the CD with your data.
These don't allow you to "export" the dicom images in a format that can be read by the 3D sequencing program. ,, Start with the Axial 3D SPGR 1mm 512x512 series.
Scroll your mouse up and down to see each image in the series.
You could have hundreds of slices.
Right Click on image and select "Export".
Export all dicom images to a new folder named "Date of Scan
- Modality
- resolution" or "2013.06.04 AX SPGR 1mm" This is important because you will probably be measuring the tumor over time. ,, The latest version
2.4 is giving me distortions on Sagital and Coronal views.
This is being built by the University of Pennsylvania and works great. , Select the Onis export folder you created. -
Step 3: Get CD of Dicom data from Radiologist.
-
Step 4: Upload contents of CD to Dropbox or Google Drive.
-
Step 5: Install "ONIS" free DICOM viewer version on PC.
-
Step 6: Set the "Paths" in ONIS to your dropbox folder location on your local PC.
-
Step 7: Double click on the best study for 3D.
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Step 8: Click OPEN and change the name of the folder Onis created to the "2013.06
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Step 9: Install "ITK-Snap" 2.2 free version.
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Step 10: Click on File/Load from Image.
Detailed Guide
This is becoming common because surgeons are using image guided surgery software in the OR.
The protocol is 1mm slices, no spacing, 512x512 resolution, contrast injection.
If you don't get good data, you can't get a 3D volume.
This will probably be an Axial 3D SPGR 1mm no spacing if you instructed the radtech to do it.
It is best to get a 3D scan in all three planes, Axial, Sagital and Coronal.
The Radiologist doesn't know how to operated the MRI machine or software so you need to instruct the RadTech what you want.
Radiologist like to "reformat" a scan.
This doesn't give good 3D data for sequencing.
You can also ask to scan only the region of the tumor.
This is a new function on GE scanners and most Rad Techs know what to do, but the radiologists are lost because this wasn't a function they had in the film days of past.
They are used to looking at the entire head, instead of just the region where the tumor is. , This should be the easy part, but the Radtech can't bill for this and the front office girls aren't computer literate, so it ends up being difficult.
They are required to do it now, so insist.
Radiologists are very protective of their data.
The good thing, is it isn't their data, it is yours. , Having it on the cloud will allow you to access it from any device. , They don't have a MAC version yet.
Most Radiologists are giving a free version of a viewer on the CD with your data.
These don't allow you to "export" the dicom images in a format that can be read by the 3D sequencing program. ,, Start with the Axial 3D SPGR 1mm 512x512 series.
Scroll your mouse up and down to see each image in the series.
You could have hundreds of slices.
Right Click on image and select "Export".
Export all dicom images to a new folder named "Date of Scan
- Modality
- resolution" or "2013.06.04 AX SPGR 1mm" This is important because you will probably be measuring the tumor over time. ,, The latest version
2.4 is giving me distortions on Sagital and Coronal views.
This is being built by the University of Pennsylvania and works great. , Select the Onis export folder you created.
About the Author
Julie Wells
Experienced content creator specializing in creative arts guides and tutorials.
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