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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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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:
External Email - Use Caution
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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Douglas N. Greve