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Hi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see the lesions volume. But when i extract lesions seprately as a new file we know that it uses the label 99 for extraction. But when i calculate the volume of this extracted lesions which i created it seprately. The volume of these two results are not the same. The volume of extracted lesions seprately is higher than what samseg automatically calculated in .stats file. Why is this happened? Why the volumes are not the same. And how can i calculate the lesions volume from extracted file that i created which is a flair that i masked with label 99? How can i recalculate the lesions volume from just exracted lesions filr without using samseg?
Thanks a lot for your help
Internally, samseg uses partial volume to compute a more accurate volume. They should still be very close though.
On 11/16/2023 6:46 AM, reza razmara wrote:
External Email - Use Caution
Hi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see the lesions volume. But when i extract lesions seprately as a new file we know that it uses the label 99 for extraction. But when i calculate the volume of this extracted lesions which i created it seprately. The volume of these two results are not the same. The volume of extracted lesions seprately is higher than what samseg automatically calculated in .stats file. Why is this happened? Why the volumes are not the same. And how can i calculate the lesions volume from extracted file that i created which is a flair that i masked with label 99? How can i recalculate the lesions volume from just exracted lesions filr without using samseg?
Thanks a lot for your help
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Thanks
The volume of lesions in label 99 in seg.mgz result is 745 mm^3.
The samseg output for lesions in samseg.stats is 633 mm^3. Is it ok?
On Thu, Nov 16, 2023, 5:57 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Internally, samseg uses partial volume to compute a more accurate volume. They should still be very close though.
On 11/16/2023 6:46 AM, reza razmara wrote:
External Email - Use CautionHi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see the lesions volume. But when i extract lesions seprately as a new file we know that it uses the label 99 for extraction. But when i calculate the volume of this extracted lesions which i created it seprately. The volume of these two results are not the same. The volume of extracted lesions seprately is higher than what samseg automatically calculated in .stats file. Why is this happened? Why the volumes are not the same. And how can i calculate the lesions volume from extracted file that i created which is a flair that i masked with label 99? How can i recalculate the lesions volume from just exracted lesions filr without using samseg?
Thanks a lot for your help
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/15CTCr2koJ0pCHfaAX203c2eT8qJQwcndNFO0I-tV8amyEz... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1F2NxclipTs9ebvlCQMzVboE5w-Td04Btx-V-1gnvOu3GS5... < https://secure-web.cisco.com/1F2NxclipTs9ebvlCQMzVboE5w-Td04Btx-V-1gnvOu3GS5... .
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Hi Reza,
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 didn'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 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 Thu, Nov 16, 2023 at 9:45 AM reza razmara rrazmara1992@gmail.com wrote:
External Email - Use CautionThanks
The volume of lesions in label 99 in seg.mgz result is 745 mm^3.
The samseg output for lesions in samseg.stats is 633 mm^3. Is it ok?
On Thu, Nov 16, 2023, 5:57 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Internally, samseg uses partial volume to compute a more accurate volume. They should still be very close though.
On 11/16/2023 6:46 AM, reza razmara wrote:
External Email - Use CautionHi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see the lesions volume. But when i extract lesions seprately as a new file we know that it uses the label 99 for extraction. But when i calculate the volume of this extracted lesions which i created it seprately. The volume of these two results are not the same. The volume of extracted lesions seprately is higher than what samseg automatically calculated in .stats file. Why is this happened? Why the volumes are not the same. And how can i calculate the lesions volume from extracted file that i created which is a flair that i masked with label 99? How can i recalculate the lesions volume from just exracted lesions filr without using samseg?
Thanks a lot for your help
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Douglas N. Greve -
Koen Van Leemput -
reza razmara