Hi Randy,
"seg.mgz" is the "hard segmentation", with lesion labeled as 99.
You have all the volumes in "samseg.stats".
If you want segmentation maps (values between 0 and 1), you should add the flag --save-posteriors to run_samseg. They will be saved in the samseg output directory under the "posteriors" folder.
You can get a lesion segmentation mask by binarizing the lesion probability map with mri_binarize.
Best, Stefano
Dear experts
I was able to get SAMSEG --lesion to work on WSL (did not crash once I used float images instead of 16bit usign), but all that's being written out are listed below:
Folder: D:\0007_Subjects-FS\T1T2-lesion-float\ Files: cost.txt gaussians.rescaled.txt mode01_bias_corrected.mgz mode01_bias_field.mgz mode01_scaling.txt mode02_bias_corrected.mgz mode02_bias_field.mgz mode02_scaling.txt samseg.stats samseg.talairach.lta sbtiv.stats seg.mgz template.lta template_coregistered.mgz template_transforms.mat Since this is the first time got --lesion to run, I have no idea what the output "should" be.? Shouldn't some sort "lesion mask" be written out? Thanks in advance for any insights/comments you might have -Randy
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX SNIPPET FROM THE END OF THE "SUCCESSFUL" SAMSEG --lesion run XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
run_samseg -o $SUBJECTS_DIR/T1T2-lesion-float -i o_ADNI_002_S_4654__MRI-m072_float.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR_float.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7
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Sample 44 times Sample 45 times Sample 46 times Sample 47 times Sample 48 times Sample 49 times Sample 50 times thresholding posterior of? Lesions with threshold: 0.7 Constructing image-to-world transform from header information (o_ADNI_002_S_4654__MRI-m072_float.nii) Read image: o_ADNI_002_S_4654__MRI-m072_float.nii using default intracranial structures to compute sbtiv measure run_samseg complete: 0:34:36.159030 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$
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YAY! ....................................
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