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You can move your ADC volumes into the output synthseg space with
mri_vol2vol --mov adc.mgz --regheader --targ synthseg.mgz --o
adc.synthseg.mgz
Then they will be voxel-for-voxel alignment
On 4/24/2023 10:16 AM, bar gen wrote:
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Dear Freesurfer experts,
I hope this email finds you well. I am writing to seek your advice on
a specific issue regarding a pediatric brain tumor and control group
dataset that I am working with. The dataset consists of
diffusion-weighted images (DWIs) with T2, b0, and b1000 trace images.
My goal is to automatically calculate the Apparent Diffusion
Coefficient (ADC) values in the contralateral white matter of both the
childhood tumor and control groups. I have considered using b0 images
segmented by SynthSeg to obtain the white matter images and then
perform the measurement. However, I am not sure if this is the correct
approach.
When I use SynthSeg, the initial segmentation output has a resolution
of 1x1x1 mm, while the ADC images have a resolution of 1.5x1.5x5 mm. I
am unsure how to overcome this discrepancy in resolution.
I would appreciate any guidance on whether using SynthSeg for
segmenting the b0 images is the correct approach, as well as any
suggestions for addressing the resolution discrepancy between the
segmentation and ADC images. Additionally, if there are alternative
methods or tools for automatically calculating ADC values in the
contralateral white matter, I would be grateful for your recommendations.
Kind regards.
Barış
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