[FreeSurfer] Lesion detection at different thresholds

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Krystal Xiwing Yau

7 Jan 2024 7 Jan '24

11:04 p.m.

External Email - Use Caution

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:

[cid:abc00aac-cc49-4ef4-9cca-50c4bf72188b]

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

[cid:7e206b3b-741a-497a-aec8-5bef569267b7]

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 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Koen Van Leemput

17 Jan 17 Jan

3:56 a.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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:

...

    External Email - Use Caution
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 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SQ0_HocLG1cW0ICC6TL2w0TL2FFAKsKAamGEcm4wR86sQf...

Krystal Xiwing Yau

21 Jan 21 Jan

8:55 p.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:ii_18d169fa598f456b1e51]

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

[cid:ii_18d169fa59af456b1e52]

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:

Thank you for your attention.

Regards, Krystal

Koen Van Leemput

29 Jan 29 Jan

10 a.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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:

...

    External Email - Use Caution
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
    External Email - Use Caution
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:

...
    External Email - Use Caution
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 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1oVh9-LtjvJeJyKSjDrCEacVV9HgKgtyUvtK2qGUrFhw4SB... https://secure-web.cisco.com/1SQ0_HocLG1cW0ICC6TL2w0TL2FFAKsKAamGEcm4wR86sQfp5_ugmBUW4fkaDUws0L9UHGmUEhef_ZZcxvw-nHVPCjX1HWUVu0jWW9czm6Ersv6PPF8myLxBglhGZZhbBDYaM2Ko6W5MRmQ0Oye4E6Ls4xH0KUFtlTCR4-hjZiBJnQXK0nMbbvZeHRezRBSvtjMqW1n96FplZLs2jv2vlkZgOyU4Jwoi8UeYGv5aZh9aVD4V2UF2_4RSxj0yVhKNpTn6_BrH2EDJG5zxvJlRgVW7teXeMbghE2nRSzuCo01CgpUlzEK8mKVI1MgEpzkPISoZGIEwqWU0_LAekOABZgA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Krystal Xiwing Yau

11 Mar 11 Mar

1:39 a.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Yes, I meant whether changing the threshold of samseg that labels lesions would change the voxel count. I have rerun the command with different thresholds, and compared with each other. The lesions volume does not change. The thresholds that I tried out were 0.3 (default), 0.7, and 0.9. The original lesion mask found to be more false positive, so I tweeked it up.

Could you please advise?

Thank you.

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: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:ii_18d55baf9b9f456b1e51]

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

[cid:ii_18d55baf9baf456b1e52]

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:

Thank you for your attention.

Regards, Krystal

Krystal Xiwing Yau

17 Mar 17 Mar

11:58 p.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Dear FreeSurfer experts,

May I know if anyone can help with this matter? I am still exploring my way to fix the lesions volume. I have inspected the raw images (FLAIR T2 images) which did not show any missing brain structures. However, the contrast of FLAIR images may be too high thus the lesions masks appear to be very false positive. In hopes of reducing the probability of false positive, I tweeked up the threshold in samseg command. Unfortunately, the lesions masks did not improve.

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

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: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:ii_18d55baf9b9f456b1e51]

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

[cid:ii_18d55baf9baf456b1e52]

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:

Thank you for your attention.

Regards, Krystal

Koen Van Leemput

18 Mar 18 Mar

2:07 p.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

I'm afraid I don't quite understand what you're asking. In your original email, you used two different thresholds and the results you showed indicated that the method worked as expected. One issue was that the lesion volume reported in .stats file is independent of the threshold used (obviously not ideal, will be changed in future versions), so that you'd need to count voxels labeled as lesion (value 99) yourself (e.g., using "mri_segstats --seg seg.mgz--o tmp.txt"). Can you please clarify what the problem is?

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau krystaly@hku.hk wrote:

...

    External Email - Use Caution
Dear FreeSurfer experts,

May I know if anyone can help with this matter? I am still exploring my way to fix the lesions volume. I have inspected the raw images (FLAIR T2 images) which did not show any missing brain structures. However, the contrast of FLAIR images may be too high thus the lesions masks appear to be very false positive. In hopes of reducing the probability of false positive, I tweeked up the threshold in samseg command. Unfortunately, the lesions masks did not improve.

Please kindly advise.

Sincerely,

Krystal

*From:* Krystal Xiwing Yau *Sent:* 11 March 2024 13:39 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Yes, I meant whether changing the threshold of samseg that labels lesions would change the voxel count. I have rerun the command with different thresholds, and compared with each other. The lesions volume does not change. The thresholds that I tried out were 0.3 (default), 0.7, and 0.9. The original lesion mask found to be more false positive, so I tweeked it up.

Could you please advise?

Thank you.

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:* 29 January 2024 23:00:08 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
    External Email - Use Caution
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:

...
    External Email - Use Caution
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
    External Email - Use Caution
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:

...
    External Email - Use Caution
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 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1UAujb2r39hfyrzCOXnNYtW-hypO4tWov_RmjYosInRKliP... https://secure-web.cisco.com/1SQ0_HocLG1cW0ICC6TL2w0TL2FFAKsKAamGEcm4wR86sQfp5_ugmBUW4fkaDUws0L9UHGmUEhef_ZZcxvw-nHVPCjX1HWUVu0jWW9czm6Ersv6PPF8myLxBglhGZZhbBDYaM2Ko6W5MRmQ0Oye4E6Ls4xH0KUFtlTCR4-hjZiBJnQXK0nMbbvZeHRezRBSvtjMqW1n96FplZLs2jv2vlkZgOyU4Jwoi8UeYGv5aZh9aVD4V2UF2_4RSxj0yVhKNpTn6_BrH2EDJG5zxvJlRgVW7teXeMbghE2nRSzuCo01CgpUlzEK8mKVI1MgEpzkPISoZGIEwqWU0_LAekOABZgA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Krystal Xiwing Yau

19 Mar 19 Mar

3:49 a.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

I tried to use mri_binarize and mri_segstats for calculating the lesions, and found it confusing with respect of the usage of mri_segstats. There's an option --seg and I input seg.mgz for that, but there's no label 99 in the file. As a result, I still have no new volume of lesions generated.

Moreover, as I want to make sure that I will get the correct count of voxels after adjusting the threshold, I view it with freeview but only a white block shown. I am not sure whether I have it fixed correctly.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

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: 19 March 2024 02:07:44 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:ii_18e52b81200f456b1e51]

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

[cid:ii_18e52b81201f456b1e52]

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:

Thank you for your attention.

Regards, Krystal

Koen Van Leemput

25 Mar 25 Mar

6:11 a.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau krystaly@hku.hk wrote:

...

    External Email - Use Caution
Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

I tried to use mri_binarize and mri_segstats for calculating the lesions, and found it confusing with respect of the usage of mri_segstats. There's an option --seg and I input seg.mgz for that, but there's no label 99 in the file. As a result, I still have no new volume of lesions generated.

Moreover, as I want to make sure that I will get the correct count of voxels after adjusting the threshold, I view it with freeview but only a white block shown. I am not sure whether I have it fixed correctly.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

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:* 19 March 2024 02:07:44 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
    External Email - Use Caution
Hi Krystal,

I'm afraid I don't quite understand what you're asking. In your original email, you used two different thresholds and the results you showed indicated that the method worked as expected. One issue was that the lesion volume reported in .stats file is independent of the threshold used (obviously not ideal, will be changed in future versions), so that you'd need to count voxels labeled as lesion (value 99) yourself (e.g., using "mri_segstats --seg seg.mgz--o tmp.txt"). Can you please clarify what the problem is?

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau krystaly@hku.hk wrote:

...
    External Email - Use Caution
Dear FreeSurfer experts,

May I know if anyone can help with this matter? I am still exploring my way to fix the lesions volume. I have inspected the raw images (FLAIR T2 images) which did not show any missing brain structures. However, the contrast of FLAIR images may be too high thus the lesions masks appear to be very false positive. In hopes of reducing the probability of false positive, I tweeked up the threshold in samseg command. Unfortunately, the lesions masks did not improve.

Please kindly advise.

Sincerely,

Krystal

*From:* Krystal Xiwing Yau *Sent:* 11 March 2024 13:39 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Yes, I meant whether changing the threshold of samseg that labels lesions would change the voxel count. I have rerun the command with different thresholds, and compared with each other. The lesions volume does not change. The thresholds that I tried out were 0.3 (default), 0.7, and 0.9. The original lesion mask found to be more false positive, so I tweeked it up.

Could you please advise?

Thank you.

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:* 29 January 2024 23:00:08 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
    External Email - Use Caution
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:

...
    External Email - Use Caution
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
    External Email - Use Caution
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:

...
    External Email - Use Caution
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 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1RyB2K4BuANnRGkfUQPVPfVhZ_qhh1Br1fOjr3tmeV9H2B_... https://secure-web.cisco.com/1SQ0_HocLG1cW0ICC6TL2w0TL2FFAKsKAamGEcm4wR86sQfp5_ugmBUW4fkaDUws0L9UHGmUEhef_ZZcxvw-nHVPCjX1HWUVu0jWW9czm6Ersv6PPF8myLxBglhGZZhbBDYaM2Ko6W5MRmQ0Oye4E6Ls4xH0KUFtlTCR4-hjZiBJnQXK0nMbbvZeHRezRBSvtjMqW1n96FplZLs2jv2vlkZgOyU4Jwoi8UeYGv5aZh9aVD4V2UF2_4RSxj0yVhKNpTn6_BrH2EDJG5zxvJlRgVW7teXeMbghE2nRSzuCo01CgpUlzEK8mKVI1MgEpzkPISoZGIEwqWU0_LAekOABZgA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1RyB2K4BuANnRGkfUQPVPfVhZ_qhh1Br1fOjr3tmeV9H2B_... 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/1qnM2k2b5_kE14xF2VzShAuQvdPuo1_6rQiNhoqK9nCeUmX... < https://secure-web.cisco.com/1qnM2k2b5_kE14xF2VzShAuQvdPuo1_6rQiNhoqK9nCeUmX... .

Krystal Xiwing Yau

26 Mar 26 Mar

4:29 a.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in posteriors folder.

As I am inspecting whether the lesions are segmented accurately, the lesions mask (with default threshold) is rather be oversensitive. I tried to view the binarized image, which is in NifTi format, but I can't view it on Freeview. How I can know if adjusting the threshold with mri_binarize would make my lesions accurately estimated afterwards?

Thank you for your kind attention.

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: 25 March 2024 18:11:42 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 19 March 2024 02:07:44 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:ii_18e74e42c2ef456b1e51]

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

[cid:ii_18e74e42c2ff456b1e52]

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:

Thank you for your attention.

Regards, Krystal

Douglas N. Greve

29 Mar 29 Mar

4:57 p.m.

Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

...

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in /posteriors/ folder.

Thank you for your kind attention.

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:* 25 March 2024 18:11:42 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau krystaly@hku.hk wrote:

        External Email - Use Caution

Dear Koen,


Apologies for any confusion caused. I'm pretty new to the program
and self-learning here.


I tried to use mri_binarize and mri_segstats for calculating the
lesions, and found it confusing with respect of the usage of
mri_segstats. There's an option --seg and I input seg.mgz for
that, but there's no label 99 in the file. As a result, I still
have no new volume of lesions generated.


Moreover, as I want to make sure that I will get the correct count
of voxels after adjusting the threshold, I view it with freeview
but only a white block shown. I am not sure whether I have it
fixed correctly.


mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o
binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o
lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg
yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt


Did I miss anything here? Please advise.


Thanks.


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:* 19 March 2024 02:07:44
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
different thresholds

        External Email - Use Caution

Hi Krystal,

I'm afraid I don't quite understand what you're asking. In your
original email, you used two different thresholds and the results
you showed indicated that the method worked as expected. One issue
was that the lesion volume reported in .stats file is independent
of the threshold used (obviously not ideal, will be changed in
future versions), so that you'd need to count voxels labeled as
lesion (value 99) yourself (e.g., using "mri_segstats --seg
seg.mgz--o tmp.txt"). Can you please clarify what the problem is?

Thanks,

Koen




On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau
<krystaly@hku.hk> wrote:

            External Email - Use Caution

    Dear FreeSurfer experts,


    May I know if anyone can help with this matter? I am still
    exploring my way to fix the lesions volume. I have inspected
    the raw images (FLAIR T2 images) which did not show any
    missing brain structures. However, the contrast of FLAIR
    images may be too high thus the lesions masks appear to be
    very false positive. In hopes of reducing the probability of
    false positive, I tweeked up the threshold in samseg command.
    Unfortunately, the lesions masks did not improve.


    Please kindly advise.


    Sincerely,

    Krystal



    ------------------------------------------------------------------------
    *From:* Krystal Xiwing Yau
    *Sent:* 11 March 2024 13:39
    *To:* Freesurfer support list
    *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
    different thresholds

    Dear Koen,


    Sorry for the late reply. I've been busy with other project.


    Yes, I meant whether changing the threshold of samseg that
    labels lesions would change the voxel count. I have rerun the
    command with different thresholds, and compared with each
    other. The lesions volume does not change. The thresholds that
    I tried out were 0.3 (default), 0.7, and 0.9. The original
    lesion mask found to be more false positive, so I tweeked it up.


    Could you please advise?


    Thank you.


    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:* 29 January 2024 23:00:08
    *To:* Freesurfer support list
    *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
    different thresholds

            External Email - Use Caution

    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:

                External Email - Use Caution

        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

                External Email - Use Caution

        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:

                    External Email - Use Caution

            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
            Fax: +852 2872 5828
            Address: Room 304, 3/F, New Clinical Building, 102
            Pokfulam Road, Hong Kong.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Martin Juneja

1 Apr 1 Apr

8:40 p.m.

New subject: [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Koen and Doug,

I am trying to do similar analysis but when I run run_samseg command, it gives me error "Illegal Instruction: 4"

I am using the FreeSurfer 7.4.1 version on Apple M2 Max MacBook Pro 14.4.1.

Is it because run_samseg is incompatible with Apple M2? If so, could you please suggest any solution (if available) how I can run run_samseg on my Apple M2 computer?

Thanks.

On Fri, Mar 29, 2024 at 3:58 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

...

Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:
    External Email - Use Caution
Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in *posteriors* folder.

As I am inspecting whether the lesions are segmented accurately, the lesions mask (with default threshold) is rather be oversensitive. I tried to view the binarized image, which is in NifTi format, but I can't view it on Freeview. How I can know if adjusting the threshold with mri_binarize would make my lesions accurately estimated afterwards?

Thank you for your kind attention.

Best regards,

Krystal

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koen Van Leemput leempko@gmail.com leempko@gmail.com *Sent:* 25 March 2024 18:11:42 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
    External Email - Use Caution
Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau krystaly@hku.hk wrote:

...
    External Email - Use Caution
Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

I tried to use mri_binarize and mri_segstats for calculating the lesions, and found it confusing with respect of the usage of mri_segstats. There's an option --seg and I input seg.mgz for that, but there's no label 99 in the file. As a result, I still have no new volume of lesions generated.

Moreover, as I want to make sure that I will get the correct count of voxels after adjusting the threshold, I view it with freeview but only a white block shown. I am not sure whether I have it fixed correctly.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

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:* 19 March 2024 02:07:44 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
    External Email - Use Caution
Hi Krystal,

I'm afraid I don't quite understand what you're asking. In your original email, you used two different thresholds and the results you showed indicated that the method worked as expected. One issue was that the lesion volume reported in .stats file is independent of the threshold used (obviously not ideal, will be changed in future versions), so that you'd need to count voxels labeled as lesion (value 99) yourself (e.g., using "mri_segstats --seg seg.mgz--o tmp.txt"). Can you please clarify what the problem is?

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau krystaly@hku.hk wrote:

...
    External Email - Use Caution
Dear FreeSurfer experts,

May I know if anyone can help with this matter? I am still exploring my way to fix the lesions volume. I have inspected the raw images (FLAIR T2 images) which did not show any missing brain structures. However, the contrast of FLAIR images may be too high thus the lesions masks appear to be very false positive. In hopes of reducing the probability of false positive, I tweeked up the threshold in samseg command. Unfortunately, the lesions masks did not improve.

Please kindly advise.

Sincerely,

Krystal

*From:* Krystal Xiwing Yau *Sent:* 11 March 2024 13:39 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Yes, I meant whether changing the threshold of samseg that labels lesions would change the voxel count. I have rerun the command with different thresholds, and compared with each other. The lesions volume does not change. The thresholds that I tried out were 0.3 (default), 0.7, and 0.9. The original lesion mask found to be more false positive, so I tweeked it up.

Could you please advise?

Thank you.

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:* 29 January 2024 23:00:08 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds
    External Email - Use Caution
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:

...
    External Email - Use Caution
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
    External Email - Use Caution
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:

...
    External Email - Use Caution
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

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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/1Tsxw9BeFdghJWdOpDgb3gh8XosoJxbDH1kgPsP8oDvqWl0... 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/1ZhJVCcRbSFshxWXFVJiIeb7fKvycCMUGQlMWS0a-xUBtXS... < https://secure-web.cisco.com/1ZhJVCcRbSFshxWXFVJiIeb7fKvycCMUGQlMWS0a-xUBtXS... .

Krystal Xiwing Yau

11:33 p.m.

New subject: Lesion detection at different thresholds

External Email - Use Caution

Dear Douglas,

Thank you for your reply.

I do not see 77, and neither does a label named "Lesions". How else can I know the lesions mask is correct? I see the lesion volume after adjusting the threshold has been decreased, but I would like to know how accurately the lesions.mgz detects the lesions on FLAIR T2 image.

Did I miss something when I execute run_samseg? I have atteched the data file generated by executing mri_segstats and the samseg processes I have made to this email for your reference.

The software and OS that I am using are listed below as well:

FreeSurfer: version 7.3.2

Linux: Ubuntu 23.04

Thank you again for your attention. Your help is highly appreciated.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 30 March 2024 4:57 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in posteriors folder.

Thank you for your kind attention.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koen Van Leemput leempko@gmail.com mailto:leempko@gmail.com Sent: 25 March 2024 18:11:42 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 19 March 2024 02:07:44 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:part1.3406laAd.I6OCu5t1@mgh.harvard.edu]

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

[cid:part2.LqpHST77.I6y81cpe@mgh.harvard.edu]

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:

Thank you for your attention.

Regards, Krystal

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1RrZZNZSHOqKb-I76B5irKr5mOg2T-VN9nx5_eF6Tt-BQkM...

Douglas N. Greve

2 Apr 2 Apr

9:17 a.m.

New subject: Lesion detection at different thresholds

Did you load the seg.mgz? Are there lesions labeled there? If so, click on one to see the value.

On 4/1/2024 11:33 PM, Krystal Xiwing Yau wrote:

...

External Email - Use Caution

Dear Douglas,

Thank you for your reply.

Did I miss something when I execute run_samseg? I have atteched the data file generated by executing mri_segstats and the samseg processes I have made to this email for your reference.

The software and OS that I am using are listed below as well:

FreeSurfer: version 7.3.2

Linux: Ubuntu 23.04

Thank you again for your attention. Your help is highly appreciated.

Best regards,

Krystal

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Sent:* 30 March 2024 4:57 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

...

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in /posteriors/ folder.

Thank you for your kind attention.

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau krystaly@hku.hk wrote:

        External Email - Use Caution

Dear Koen,


Apologies for any confusion caused. I'm pretty new to the program
and self-learning here.


I tried to use mri_binarize and mri_segstats for calculating the
lesions, and found it confusing with respect of the usage of
mri_segstats. There's an option --seg and I input seg.mgz for
that, but there's no label 99 in the file. As a result, I still
have no new volume of lesions generated.


Moreover, as I want to make sure that I will get the correct
count of voxels after adjusting the threshold, I view it with
freeview but only a white block shown. I am not sure whether I
have it fixed correctly.


mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o
binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o
lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg
yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt


Did I miss anything here? Please advise.


Thanks.


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:* 19 March 2024 02:07:44
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
different thresholds

        External Email - Use Caution

Hi Krystal,

I'm afraid I don't quite understand what you're asking. In your
original email, you used two different thresholds and the results
you showed indicated that the method worked as expected. One
issue was that the lesion volume reported in .stats file is
independent of the threshold used (obviously not ideal, will be
changed in future versions), so that you'd need to count voxels
labeled as lesion (value 99) yourself (e.g., using "mri_segstats
--seg seg.mgz--o tmp.txt"). Can you please clarify what the
problem is?

Thanks,

Koen




On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau
<krystaly@hku.hk> wrote:

            External Email - Use Caution

    Dear FreeSurfer experts,


    May I know if anyone can help with this matter? I am still
    exploring my way to fix the lesions volume. I have inspected
    the raw images (FLAIR T2 images) which did not show any
    missing brain structures. However, the contrast of FLAIR
    images may be too high thus the lesions masks appear to be
    very false positive. In hopes of reducing the probability of
    false positive, I tweeked up the threshold in samseg command.
    Unfortunately, the lesions masks did not improve.


    Please kindly advise.


    Sincerely,

    Krystal



    ------------------------------------------------------------------------
    *From:* Krystal Xiwing Yau
    *Sent:* 11 March 2024 13:39
    *To:* Freesurfer support list
    *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
    different thresholds

    Dear Koen,


    Sorry for the late reply. I've been busy with other project.


    Yes, I meant whether changing the threshold of samseg that
    labels lesions would change the voxel count. I have rerun the
    command with different thresholds, and compared with each
    other. The lesions volume does not change. The thresholds
    that I tried out were 0.3 (default), 0.7, and 0.9. The
    original lesion mask found to be more false positive, so I
    tweeked it up.


    Could you please advise?


    Thank you.


    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:* 29 January 2024 23:00:08
    *To:* Freesurfer support list
    *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
    different thresholds

            External Email - Use Caution

    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:

                External Email - Use Caution

        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

                External Email - Use Caution

        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:

                    External Email - Use Caution

            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
            Fax: +852 2872 5828
            Address: Room 304, 3/F, New Clinical Building, 102
            Pokfulam Road, Hong Kong.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Krystal Xiwing Yau

9:58 p.m.

New subject: Lesion detection at different thresholds

External Email - Use Caution

Dear Douglas,

Yes, I loaded seg.mgz on freeview but still no lesions labeled there.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 02 April 2024 21:17:19 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lesion detection at different thresholds

Did you load the seg.mgz? Are there lesions labeled there? If so, click on one to see the value.

On 4/1/2024 11:33 PM, Krystal Xiwing Yau wrote:

External Email - Use Caution

Dear Douglas,

Thank you for your reply.

Did I miss something when I execute run_samseg? I have atteched the data file generated by executing mri_segstats and the samseg processes I have made to this email for your reference.

The software and OS that I am using are listed below as well:

FreeSurfer: version 7.3.2

Linux: Ubuntu 23.04

Thank you again for your attention. Your help is highly appreciated.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU Sent: 30 March 2024 4:57 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in posteriors folder.

Thank you for your kind attention.

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 19 March 2024 02:07:44 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:part1.Rq9Rm61f.EAYy0Psg@mgh.harvard.edu]

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

[cid:part2.HBdQCAlc.L5ttuGM7@mgh.harvard.edu]

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:

Thank you for your attention.

Regards, Krystal

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1vkxHr26woqi5XZKIrhFf8VTP6An-8MS4M2PXkm9p7m60Hx...https://secure-web.cisco.com/1RrZZNZSHOqKb-I76B5irKr5mOg2T-VN9nx5_eF6Tt-BQkMCCCAbKs08-YYyeZZhIHxLTpWArEjD_d5cWtmI6W1RzVzgQUabgtq2NU0xKHu_SN461QC5xIj-zxkRkRvSZTUKFSgs7GSyYGWxH-UUPCKr0s9ovZk6pUABEWti9HpOpR0ONw9vcQblo6pChNgEpWG7SeKZgC2LmPgoPoesaGmXS6AI4U0wfIKZn7KuC_5qHAuLR2qYnxNuZyiWXmIX3zZ6TNQJTjzXcgze_olqLAK9Zxb7coxQXDUN9m7uNyu0Byd3Q2gMtuv5bmJuNN6NRKu_oA-Hy5mh9Y0P7HtxuUg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Douglas N. Greve

4 Apr 4 Apr

12:46 p.m.

New subject: Lesion detection at different thresholds

It may be the case that it just did not detect any lesions in the input. The lesions volume in the posterior may be empty.

On 4/2/2024 9:58 PM, Krystal Xiwing Yau wrote:

...

External Email - Use Caution

Dear Douglas,

Yes, I loaded seg.mgz on freeview but still no lesions labeled there.

Best regards,

Krystal

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Sent:* 02 April 2024 21:17:19 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Lesion detection at different thresholds Did you load the seg.mgz? Are there lesions labeled there? If so, click on one to see the value.

On 4/1/2024 11:33 PM, Krystal Xiwing Yau wrote:

...

External Email - Use Caution

Dear Douglas,

Thank you for your reply.

Did I miss something when I execute run_samseg? I have atteched the data file generated by executing mri_segstats and the samseg processes I have made to this email for your reference.

The software and OS that I am using are listed below as well:

FreeSurfer: version 7.3.2

Linux: Ubuntu 23.04

Thank you again for your attention. Your help is highly appreciated.

Best regards,

Krystal

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

...

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in /posteriors/ folder.

Thank you for your kind attention.

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau krystaly@hku.hk wrote:

        External Email - Use Caution

Dear Koen,


Apologies for any confusion caused. I'm pretty new to the
program and self-learning here.


I tried to use mri_binarize and mri_segstats for calculating the
lesions, and found it confusing with respect of the usage of
mri_segstats. There's an option --seg and I input seg.mgz for
that, but there's no label 99 in the file. As a result, I still
have no new volume of lesions generated.


Moreover, as I want to make sure that I will get the correct
count of voxels after adjusting the threshold, I view it with
freeview but only a white block shown. I am not sure whether I
have it fixed correctly.


mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o
binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o
lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg
yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt


Did I miss anything here? Please advise.


Thanks.


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:* 19 March 2024 02:07:44
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
different thresholds

        External Email - Use Caution

Hi Krystal,

I'm afraid I don't quite understand what you're asking. In your
original email, you used two different thresholds and the
results you showed indicated that the method worked as expected.
One issue was that the lesion volume reported in .stats file is
independent of the threshold used (obviously not ideal, will be
changed in future versions), so that you'd need to count voxels
labeled as lesion (value 99) yourself (e.g., using "mri_segstats
--seg seg.mgz--o tmp.txt"). Can you please clarify what the
problem is?

Thanks,

Koen




On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau
<krystaly@hku.hk> wrote:

            External Email - Use Caution

    Dear FreeSurfer experts,


    May I know if anyone can help with this matter? I am still
    exploring my way to fix the lesions volume. I have inspected
    the raw images (FLAIR T2 images) which did not show any
    missing brain structures. However, the contrast of FLAIR
    images may be too high thus the lesions masks appear to be
    very false positive. In hopes of reducing the probability of
    false positive, I tweeked up the threshold in samseg
    command. Unfortunately, the lesions masks did not improve.


    Please kindly advise.


    Sincerely,

    Krystal



    ------------------------------------------------------------------------
    *From:* Krystal Xiwing Yau
    *Sent:* 11 March 2024 13:39
    *To:* Freesurfer support list
    *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
    different thresholds

    Dear Koen,


    Sorry for the late reply. I've been busy with other project.


    Yes, I meant whether changing the threshold of samseg that
    labels lesions would change the voxel count. I have rerun
    the command with different thresholds, and compared with
    each other. The lesions volume does not change. The
    thresholds that I tried out were 0.3 (default), 0.7, and
    0.9. The original lesion mask found to be more false
    positive, so I tweeked it up.


    Could you please advise?


    Thank you.


    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:* 29 January 2024 23:00:08
    *To:* Freesurfer support list
    *Subject:* Re: [Freesurfer] [FreeSurfer] Lesion detection at
    different thresholds

            External Email - Use Caution

    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:

                External Email - Use Caution

        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

                External Email - Use Caution

        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:

                    External Email - Use Caution

            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
            Fax: +852 2872 5828
            Address: Room 304, 3/F, New Clinical Building, 102
            Pokfulam Road, Hong Kong.
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Krystal Xiwing Yau

5 Apr 5 Apr

5:09 a.m.

New subject: Lesion detection at different thresholds

External Email - Use Caution

Dear Douglas,

Thanks for your reply.

In my previous conversation with Koen, I have been having problems with the over-sensitive lesion mask as shown in Fig. 1. Nonetheless, I have adjusted the theshold while running the run_samseg command with the option of --save-posteriors. There's a file named Lesions.mgz , and the volume has been saved in stats file.

When I inspected the FLAIR reg image (Fig.2), the lesions detected by samseg had shown in areas other than where actual lesions should be. I was therefure worried that the statistics generated at the end of run_samseg was incorrect. That's why I was asking how I can ensure the new Lesion volume is accurate after running mri_binarize and mri_segstats.

As you suggested, click onto the seg.mgz to see the value on the panel. Please see Fig. 3, the lesion was not shown as 99, but 3. Moreover, I wonder if I can have the total volume of lesions from the values shown on the panel. As I looked at another successful case, like Fig. 4. The panel only shows value 99 for the lesions (Fig. 5). Would you please kindly advise?

[cid:ccf7935a-a3bf-411f-82f2-80dbe51194e1]

Fig. 1 FLAIR image with Lesion mask

[cid:b64f1880-f415-444a-9e14-4909974df2f6]

Fig. 2 FLAIR reg. image

[cid:9c3f3baa-ca18-4166-a605-df4ed8fbf635]

Fig. 3 seg.mgz of problematic case

[cid:ce6f1aa4-79ab-4b6b-ba70-1aa30c9f425d]

Fig 4. FLAIR image of successful case

[cid:f54ca04f-dde0-4010-8c71-644b87f85cd7]

Fig 5. seg.mgz of the successful case

I apologize about the lengthy email but I am pretty frustrated here as I am self-learning.

Thank you so much for your attention and time.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 05 April 2024 00:46:03 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lesion detection at different thresholds

It may be the case that it just did not detect any lesions in the input. The lesions volume in the posterior may be empty.

On 4/2/2024 9:58 PM, Krystal Xiwing Yau wrote:

External Email - Use Caution

Dear Douglas,

Yes, I loaded seg.mgz on freeview but still no lesions labeled there.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU Sent: 02 April 2024 21:17:19 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lesion detection at different thresholds

Did you load the seg.mgz? Are there lesions labeled there? If so, click on one to see the value.

On 4/1/2024 11:33 PM, Krystal Xiwing Yau wrote:

External Email - Use Caution

Dear Douglas,

Thank you for your reply.

Did I miss something when I execute run_samseg? I have atteched the data file generated by executing mri_segstats and the samseg processes I have made to this email for your reference.

The software and OS that I am using are listed below as well:

FreeSurfer: version 7.3.2

Linux: Ubuntu 23.04

Thank you again for your attention. Your help is highly appreciated.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU Sent: 30 March 2024 4:57 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

External Email - Use Caution

Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in posteriors folder.

Thank you for your kind attention.

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 19 March 2024 02:07:44 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

Hi Krystal,

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

External Email - Use Caution

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.hkmailto:krystaly@hku.hk> wrote:

External Email - Use Caution

Dear Koen,

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

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

Best regards,

Krystal

External Email - Use Caution

Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

External Email - Use Caution

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:

[cid:part1.N6OgJloo.Zhyu9Tte@mgh.harvard.edu]

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

[cid:part2.J92cPtns.NZjIr0j0@mgh.harvard.edu]

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:

Thank you for your attention.

Regards, Krystal

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Krystal Xiwing Yau

18 Apr 18 Apr

11:09 p.m.

New subject: Lesion detection at different thresholds

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To Whom It may Concern,

Just wanted to check in on this matter - how else can I check if the newly thresholded lesion mask accurately detects the lesions.

The last resort would be manually editing as I searched through the archive. If so, please advise on how to edit the lesions. Thank you.

Best regards,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 05 April 2024 17:09 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lesion detection at different thresholds

Dear Douglas,

Thanks for your reply.

When I inspected the FLAIR reg image (Fig.2), the lesions detected by samseg had shown in areas other than where actual lesions should be. I was therefore worried that the statistics generated at the end of run_samseg was incorrect. That's why I was asking how I can ensure the new Lesion volume is accurate after running mri_binarize and mri_segstats.

[cid:ccf7935a-a3bf-411f-82f2-80dbe51194e1]

Fig. 1 FLAIR image with Lesion mask

[cid:b64f1880-f415-444a-9e14-4909974df2f6]

Fig. 2 FLAIR reg. image

[cid:9c3f3baa-ca18-4166-a605-df4ed8fbf635]

Fig. 3 seg.mgz of problematic case

[cid:ce6f1aa4-79ab-4b6b-ba70-1aa30c9f425d]

Fig 4. FLAIR image of successful case

[cid:f54ca04f-dde0-4010-8c71-644b87f85cd7]

Fig 5. seg.mgz of the successful case

I apologize about the lengthy email but I am pretty frustrated here as I am self-learning.

Thank you so much for your attention and time.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 05 April 2024 00:46:03 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lesion detection at different thresholds

It may be the case that it just did not detect any lesions in the input. The lesions volume in the posterior may be empty.

On 4/2/2024 9:58 PM, Krystal Xiwing Yau wrote:

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Dear Douglas,

Yes, I loaded seg.mgz on freeview but still no lesions labeled there.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU Sent: 02 April 2024 21:17:19 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lesion detection at different thresholds

Did you load the seg.mgz? Are there lesions labeled there? If so, click on one to see the value.

On 4/1/2024 11:33 PM, Krystal Xiwing Yau wrote:

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Dear Douglas,

Thank you for your reply.

Did I miss something when I execute run_samseg? I have atteched the data file generated by executing mri_segstats and the samseg processes I have made to this email for your reference.

The software and OS that I am using are listed below as well:

FreeSurfer: version 7.3.2

Linux: Ubuntu 23.04

Thank you again for your attention. Your help is highly appreciated.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU Sent: 30 March 2024 4:57 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Just load the seg.mgz and click on a voxel in the lesion, then look at the value in the panel. There is a slight chance it could be 77 instead of 99.

On 3/26/2024 4:29 AM, Krystal Xiwing Yau wrote:

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Dear Koen,

Thank you so much for your clarification. The volume changed after running the suggested commands.

It's weird that the label 99 does not exist in my seg.mgz, but I still see my lesions.mgz in posteriors folder.

Thank you for your kind attention.

Best regards,

Krystal

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Hi Krystal,

Sorry I should have been more specific. When you do

mri_segstats --seg seg.mgz --o tmp.txt

the label 99 will be indicated in the second column. E.g., "39 99 9157 10384.1 Seg0099" means that there are 9157 voxels labeled as lesion, with a volume of 10384.1 mm^3.

To do the thresholding on the posteriors, you can do (for example):

mri_binarize --i Lesions.mgz --min 0.9 --o thresholded_0pt9.mgz

Subsequently the lesion volume can be counted by doing

mri_segstats --seg thresholded_0pt9.mgz --o tmp_0pt9.txt

which will create a line of the form

2 1 6301 7145.4 Seg0001

which indicates 6301 voxels with volume 7145.4mm^3 with label 1 (all the other voxels in the image being labeled 0 after the mri_binarize command).

I hope this clarifies things for you,

Koen

On Tue, Mar 19, 2024 at 3:50 AM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

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Dear Koen,

Apologies for any confusion caused. I'm pretty new to the program and self-learning here.

mri_binarize --i samsegoutput/posteriors/Lesions.mgz --o binarized_lesions_threshold0.7.mgz --min 0.7

mri_binarize --i binarized_lesions_threshold0.7.mgz --o lesions_label_0.7.mgz --match 99

mri_segstats --i binarized_lesions_threshold0.7.mgz --seg yourSeg/seg.mgz --sum lesion_stats_threshold0.7.txt

Did I miss anything here? Please advise.

Thanks.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 19 March 2024 02:07:44 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

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Hi Krystal,

Thanks,

Koen

On Sun, Mar 17, 2024 at 11:59 PM Krystal Xiwing Yau <krystaly@hku.hkmailto:krystaly@hku.hk> wrote:

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Dear FreeSurfer experts,

Please kindly advise.

Sincerely,

Krystal

________________________________ From: Krystal Xiwing Yau Sent: 11 March 2024 13:39 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

Dear Koen,

Sorry for the late reply. I've been busy with other project.

Could you please advise?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koen Van Leemput <leempko@gmail.commailto:leempko@gmail.com> Sent: 29 January 2024 23:00:08 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Lesion detection at different thresholds

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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.hkmailto: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.

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

Best regards,

Krystal

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Hi Krystal,

Apologies for the delay in replying (grant deadline).

Hope this helps,

Koen

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

[cid:part1.N6OgJloo.Zhyu9Tte@mgh.harvard.edu]

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

[cid:part2.J92cPtns.NZjIr0j0@mgh.harvard.edu]

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:

Thank you for your attention.

Regards, Krystal