Am I right to assume that you put the ADC image into samseg? I'm not
sure I've seen that before. If you have an anatomical, I would run
samseg on that, then use mri_coreg (or bbregister if you ran it through
recon-all) to register the anat to the ADC, then use mri_vol2vol to map
the seg to the ADC space, then use that as for your ROI analysis. I'm
not sure about your bias field correction question. If you run the
analysis as I suggest, then there is not the option, which is probably
the cleanest way to do it. If you want to let samseg do the bias
correction, you will need to undo the scaling (I think there is a text
file called scalefactor.txt or some such)
On 5/27/2025 11:43 AM, Taghizadeh Mortezaei, Nima wrote:
Hello everyone,
I am currently working with ADC values extracted from inhomogeneity
bias-corrected ADC MRIs obtained through SAMSEG and have encountered a
few issues that I would greatly appreciate your insights on.
1.
Units for ADC Values: When extracting ADC values for my ROIs,
using 3D Slicer, I noticed that no unit was provided for the ADC
values, neither in the software nor in the imaging visualization
tools (PACS, VISAGE). I also checked the DICOM metadata for ADC
and DWI MRIs but could not find any relevant tags related to ADC
values, rescaling, or intersection. As a result, I am uncertain
about the unit or scale used for the ADC values.
2.
Discrepancy in ADC Value Range: The mean ADC values extracted from
the bias-corrected image for my ROIs were in the range of 150-250.
These values seem far away from the normal average ADC values for
these structures. I suspected that the bias correction might have
influenced these values, so I also extracted the values from the
original ADC image. In this case, the values ranged from 1200-1500
for ROIs. However, I still could not identify any unit or
rescaling factor.
Considering that the average normal ADC values for my ROI are around
1000 to 1500 x 10^-6 mm²/s, I have two questions:
For extracting radiomics features (including ADC values) from the ADC
image, would you recommend using the bias-corrected image or the
original ADC image as the scalar volume?
Based on the values I found, there must be a rescaling factor (like
10^-6 ). Would you happen to know where I might find the rescaling
factor, or how I could confirm it?
I would greatly appreciate any guidance you could provide on these issues.
Thanks,
Nima
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