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 $SUBJECTS_DIR/T1T2-lesion-float -i o_ADNI_002_S_4654__MRI-m072_float.nii rT1_o_ADNI_002_S_4654__MRI-m072_FLAIR_float.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 .................................... .................................... Sample 44 times Sample 45 times Sample 46 times Sample 47 times Sample 48 times Sample 49 times Sample 50 times thresholding posterior of? Lesions with threshold: 0.7 Constructing image-to-world transform from header information (o_ADNI_002_S_4654__MRI-m072_float.nii) Read image: o_ADNI_002_S_4654__MRI-m072_float.nii using default intracranial structures to compute sbtiv measure run_samseg complete: 0:34:36.159030 daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ .................................... YAY! .................................... XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20220310/462228f1/attachment-0001.html
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