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Hi Krystal,

I'm not sure I understand -- changing the threshold should change the number of voxels labeled as lesion in seg.mgz. Can you confirm that we're talking about the same thing?

Thanks,

Koen


On Sun, Jan 21, 2024 at 8:56 PM Krystal Xiwing Yau <krystaly@hku.hk> wrote:

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Dear Koen,


Thank you for your reply and wish you the best of luck on your grant application.


As some of the lesion masks are found to be weird, which shows false positive lesions on the brain, I increased the threshold to lower false positive results. The number of lesion volume and the lesion mask did not show the difference between two different thresholded images, though. Is it normal to have lesion volume the same even with a different threshold?


I look forward to hearing from you. Thank you so much for your time and patience.


Best regards,

Krystal

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.com>
Sent: 17 January 2024 16:56:34
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
 

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Hi Krystal,

Apologies for the delay in replying (grant deadline).

The lesion class in samseg is a bit special, as the internal lesion probabilities are thresholded (using the value passed on via the --threshold flag, or a default value 0.3 if you don't use that flag) to obtain the voxels labeled as 99 in the segmentation output. In contrast, the value in the .stats file is simply the sum (over all voxels) of those internal lesion probabilities.

If you want to inspect the impact of the exact threshold value on the number of voxels with label 99, you could run (as you did) samseg with the --save-posteriors flag to save the internal lesion probabilities (in yourSeg/posteriors/Lesions.mgz). Then you can play with mri_binarize and mri_segstats to obtain lesion volumes for different thresholds without having to re-run sameg anew.

Hope this helps,

Koen

On Sun, Jan 7, 2024 at 11:05 PM Krystal Xiwing Yau <krystaly@hku.hk> wrote:

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Dear FS experts,


I am testing out which threshold works the best for the image. As I tested 0.3 and 0.9, the lesion masks do show the difference but the measurement is the same. Please see below for your information:



Fig 1. Lesion.mgz with a threshold of 0.3 applied to FLAIR image 



Fig 2. Lesions.mgz with a threshold of 0.7 applied to FLAIR image


Do the volume of lesions supposedly different with threshold adjustments? 


The following code is what I used for running samseg:

run_samseg --input $FREESURFER_HOME/${i}.nii $FREESURFER_HOME/${i}_flair_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 --output $SUBJECTS_DIR/${i}_samsegOutput_thold0.7/ --save-posteriors --threads 8
Thank you for your attention.


Regards,
Krystal

Tel.: +852 2255 5024
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