Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)

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Re: freeview -ss orientation...

eTIV in SynthSeg

Ania Holubecki

3 Jun 2025 3 Jun '25

12:10 p.m.

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Hi Ruopeng,

I tried the two latest versions installed on our computing cluster:

freesurfer/7.3.2 freesurfer/8.1

The most recent development version worked - thanks so much!

*Ania Holubecki*

On Thu, May 15, 2025 at 9:10 AM freesurfer-request@nmr.mgh.harvard.edu wrote:

...

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Today's Topics:

freeview -ss orientation inconsistencies (Ania Holubecki)

Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Iglesias Gonzalez, Juan E.)

Re: Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.)

Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Douglas N. Greve)

Question on Samseg Basic and Samseg for MS lesions (Stefano Cerri)

Re: Question on Samseg Basic and Samseg for MS lesions (Arianna Menardi)

Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Payam Sadeghi Shabestari)

Re: Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.)

Re: SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are disorganized volumes usable? (Iglesias Gonzalez, Juan E.)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Nolan, Jackson)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Toms, Robert)

mri segstats "masksign abs" syntaxis option (Gonzalo Rojas Costa)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Iglesias Gonzalez, Juan E.)

Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Douglas N. Greve)

Re: Question on Samseg Basic and Samseg for MS lesions (Douglas N. Greve)

Message: 1 Date: Tue, 13 May 2025 15:23:26 -0500 From: Ania Holubecki ania.holubecki@gmail.com Subject: [Freesurfer] freeview -ss orientation inconsistencies To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CADR7LJVJ1hFA0tPR-W2uXnKwY4GGQoW= vP983k6hL4uaqAr0wg@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
    External Email - Use Caution
Hi,

I have a script that utilizes the -ss flag on the freeview command to take axial, sagittal, and coronal screenshots iteratively. I have multiple images loaded into freeview at a time for each screenshot, and most of the loaded images are the same across all the screenshots, except for one spherical ROI that is only the same within a given sagittal/axial/coronal set.

I have been encountering a problem where some of the screenshots are horizontally mirrored (left-hemisphere/right hemisphere flipped) in comparison to the rest of the images. This happens the most often for the coronal screenshot, but has also occurred for the axial screenshot. The spherical ROIs for which this mirroring occurs is not consistent - every time I run the script, it's a different set that's horizontally mirrored.

Has anyone encountered this issue and has a way to guarantee the orientation of the screenshot? Any tips are greatly appreciated!

Best,

*Ania Holubecki*

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Ania Holubecki

1 Jul 1 Jul

11:37 a.m.

New subject: freeview -ss orientation inconsistencies (Wang, Ruopeng)

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Hi,

I spoke too soon - using the developmental version of freesurfer did not work. A reminder of the issue below:

I have a script that utilizes the -ss flag on the freeview command to take axial, sagittal, and coronal screenshots iteratively. I have multiple images loaded into freeview at a time for each screenshot, and most of the loaded images are the same across all the screenshots, except for one spherical ROI that is only the same within a given sagittal/axial/coronal set.

I have been encountering a problem where some of the screenshots are horizontally mirrored (left-hemisphere/right hemisphere flipped) in comparison to the rest of the images. This happens the most often for the coronal screenshot, but has also occurred for the axial screenshot. The spherical ROIs for which this mirroring occurs is not consistent - every time I run the script, it's a different set that's horizontally mirrored.

*Ania Holubecki*

On Tue, Jun 3, 2025 at 11:10 AM Ania Holubecki ania.holubecki@gmail.com wrote:

...

Hi Ruopeng,

I tried the two latest versions installed on our computing cluster:

freesurfer/7.3.2 freesurfer/8.1

The most recent development version worked - thanks so much!

*Ania Holubecki*

On Thu, May 15, 2025 at 9:10 AM freesurfer-request@nmr.mgh.harvard.edu wrote:

...
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1R5CD0U5oUsF2bnqAnv5jl0Wac6h-u4Pkyv-NRURa-sEbYo... or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

Today's Topics:

freeview -ss orientation inconsistencies (Ania Holubecki)

Re: freeview -ss orientation inconsistencies (Wang, Ruopeng)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Iglesias Gonzalez, Juan E.)

Re: Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.)

Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Douglas N. Greve)

Question on Samseg Basic and Samseg for MS lesions (Stefano Cerri)

Re: Question on Samseg Basic and Samseg for MS lesions (Arianna Menardi)

Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Payam Sadeghi Shabestari)

Re: Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.)

Re: SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are disorganized volumes usable? (Iglesias Gonzalez, Juan E.)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Nolan, Jackson)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Toms, Robert)

mri segstats "masksign abs" syntaxis option (Gonzalo Rojas Costa)

Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Iglesias Gonzalez, Juan E.)

Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Douglas N. Greve)

Re: Question on Samseg Basic and Samseg for MS lesions (Douglas N. Greve)

Message: 1 Date: Tue, 13 May 2025 15:23:26 -0500 From: Ania Holubecki ania.holubecki@gmail.com Subject: [Freesurfer] freeview -ss orientation inconsistencies To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CADR7LJVJ1hFA0tPR-W2uXnKwY4GGQoW= vP983k6hL4uaqAr0wg@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
    External Email - Use Caution
Hi,

I have a script that utilizes the -ss flag on the freeview command to take axial, sagittal, and coronal screenshots iteratively. I have multiple images loaded into freeview at a time for each screenshot, and most of the loaded images are the same across all the screenshots, except for one spherical ROI that is only the same within a given sagittal/axial/coronal set.

I have been encountering a problem where some of the screenshots are horizontally mirrored (left-hemisphere/right hemisphere flipped) in comparison to the rest of the images. This happens the most often for the coronal screenshot, but has also occurred for the axial screenshot. The spherical ROIs for which this mirroring occurs is not consistent - every time I run the script, it's a different set that's horizontally mirrored.

Has anyone encountered this issue and has a way to guarantee the orientation of the screenshot? Any tips are greatly appreciated!

Best,

*Ania Holubecki*

Wang, Ruopeng

1:32 p.m.

New subject: freeview -ss orientation inconsistencies (Wang, Ruopeng)

Would it be possible to share the command that produced the error? Also, can you confirm what version of freeview it was? Was it 8.1 or the latest dev?

Ruopeng

On Jul 1, 2025, at 11:37 AM, Ania Holubecki <ania.holubecki@gmail.commailto:ania.holubecki@gmail.com> wrote:

External Email - Use Caution

Hi,

I spoke too soon - using the developmental version of freesurfer did not work. A reminder of the issue below:

Ania Holubecki

On Tue, Jun 3, 2025 at 11:10 AM Ania Holubecki <ania.holubecki@gmail.commailto:ania.holubecki@gmail.com> wrote: Hi Ruopeng,

I tried the two latest versions installed on our computing cluster:

freesurfer/7.3.2 freesurfer/8.1

The most recent development version worked - thanks so much!

Ania Holubecki

On Thu, May 15, 2025 at 9:10 AM <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1R5CD0U5oUsF2bnqAnv5jl0Wac6h-u4Pkyv-NRURa-sEbYoNfICUXR6brD88DmtHM8OypYuIkhlVf4z7AKM4I6ee637E2cqIhcEbQ2P-jL_08CR7F65ac0uu1tKmGU6jzruZp-wdcJiODxEIGrmIjMLRIG0t1M9YA6QkSSlkwfm0IR8Ro_Nh7DIOGDPARfV7W-Go8Fm4O_uvfrYm4H8UMmgDNg_WLrxL5WhGGMT5aOtAh_rcej5dQfWwI6dnrldwXccx5cwDebsrC4kwj4YKCqGNxdl2DaiD5AA0jbFHG4Clq3E03X3QYHaJOgdW4CzUTFTf7WmA91XuuD9c4SIqEng/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edumailto:freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

Today's Topics:

1. freeview -ss orientation inconsistencies (Ania Holubecki) 2. Re: freeview -ss orientation inconsistencies (Wang, Ruopeng) 3. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Iglesias Gonzalez, Juan E.) 4. Re: Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.) 5. Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Douglas N. Greve) 6. Question on Samseg Basic and Samseg for MS lesions (Stefano Cerri) 7. Re: Question on Samseg Basic and Samseg for MS lesions (Arianna Menardi) 8. Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Payam Sadeghi Shabestari) 9. Re: Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? (Iglesias Gonzalez, Juan E.) 10. Re: SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are disorganized volumes usable? (Iglesias Gonzalez, Juan E.) 11. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Nolan, Jackson) 12. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Toms, Robert) 13. mri segstats "masksign abs" syntaxis option (Gonzalo Rojas Costa) 14. Re: Hippocampal Subvolumes Error -- segmentHA_T1_long (Iglesias Gonzalez, Juan E.) 15. Re: Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 (Douglas N. Greve) 16. Re: Question on Samseg Basic and Samseg for MS lesions (Douglas N. Greve)

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Message: 1 Date: Tue, 13 May 2025 15:23:26 -0500 From: Ania Holubecki <ania.holubecki@gmail.commailto:ania.holubecki@gmail.com> Subject: [Freesurfer] freeview -ss orientation inconsistencies To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <CADR7LJVJ1hFA0tPR-W2uXnKwY4GGQoW=vP983k6hL4uaqAr0wg@mail.gmail.commailto:vP983k6hL4uaqAr0wg@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

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Hi,

Has anyone encountered this issue and has a way to guarantee the orientation of the screenshot? Any tips are greatly appreciated!

Best,

*Ania Holubecki* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20250513/af...http://secure-web.cisco.com/1lYZBuDDrs7tx4Uw2h8yFUYvRHc8-icdSgUHExfC4AsyQiXXw1VWRCYN81TbJn2cwTJjhTnt73fDyjMGjEOTrWeJ4fIYA6nGNPExS3K_ox3rUTkRWgRym-M6rufzr-0YfMXshFAW2IZ2n6GgGWU_CcuRjWqwDhbGUtZedEtThNwZiwUTsva7N_1sv_HeR6Fgrifg431zQUB9wY7LQahPrpUa4Ia8I6kOmUoLaZZ4du-qSKsTuYip12y5Kka5v8A7PrGqXTiLzUXQx7_2tAfDhkoFuy6ZdmHDzc-OCHj5yScJ4lfIjUiPHjs_BAkcc9gjJWz69pM1WlwdJFvi8NQcKaw/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250513%2Faf7c6a2a%2Fattachment-0001.html

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Message: 2 Date: Tue, 13 May 2025 20:58:12 +0000 From: "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Subject: Re: [Freesurfer] freeview -ss orientation inconsistencies To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <BE62734B-01FA-4EAE-97DF-FBA2554C6868@mgh.harvard.edumailto:BE62734B-01FA-4EAE-97DF-FBA2554C6868@mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii"

What version of FS are you running? Can you try the most recent development version?

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview https://secure-web.cisco.com/1AKS_DKpAqiR43janvBIENOjdYm3iQERM6ZHOJXlS2KNH2IllnREhT0nq150hhbkiXo8_-ZS0AVKtd7SArNhw1Y9RukveyO3cK3WJ17Z_J0yqwpuwZL7cXZ0wEqu3oEBVOMHx80ciA-D6l-toEOVXBTNK87sFlX5HO8CXwDahy8Y_Ad2XGfQMHA2j4i7s_jATCCct_hK8c0AUuXvgYc7yfNFU-XPRRtiaFqAcm5DyMwiontMwlaMz4yg4hYKgj2Cg53xLdsYqR-HDv_Q5xnWyfuAOnu9zLMvO9Ro3eixKy5tcE9ywJoOJN2nu6GWvEuNp58IazZvNpVAmuajQmiAa_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

Ruopeng

On May 13, 2025, at 4:23 PM, Ania Holubecki <ania.holubecki@gmail.commailto:ania.holubecki@gmail.com<mailto:ania.holubecki@gmail.commailto:ania.holubecki@gmail.com>> wrote:

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Hi,

Has anyone encountered this issue and has a way to guarantee the orientation of the screenshot? Any tips are greatly appreciated!

Best,

Ania Holubecki _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1R5CD0U5oUsF2bnqAnv5jl0Wac6h-u4Pkyv-NRURa-sEbYoNfICUXR6brD88DmtHM8OypYuIkhlVf4z7AKM4I6ee637E2cqIhcEbQ2P-jL_08CR7F65ac0uu1tKmGU6jzruZp-wdcJiODxEIGrmIjMLRIG0t1M9YA6QkSSlkwfm0IR8Ro_Nh7DIOGDPARfV7W-Go8Fm4O_uvfrYm4H8UMmgDNg_WLrxL5WhGGMT5aOtAh_rcej5dQfWwI6dnrldwXccx5cwDebsrC4kwj4YKCqGNxdl2DaiD5AA0jbFHG4Clq3E03X3QYHaJOgdW4CzUTFTf7WmA91XuuD9c4SIqEng/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Message: 3 Date: Wed, 14 May 2025 06:25:27 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: "Nolan, Jackson" <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu> Message-ID: <PH0PR04MB838880027C07BC363D671E9EFD96A@PH0PR04MB8388.namprd04.prod.outlook.commailto:PH0PR04MB838880027C07BC363D671E9EFD96A@PH0PR04MB8388.namprd04.prod.outlook.com>

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Thanks for catching this, Robert. It?s a small bug that does not affect the results on the cases that didn?t crash. Jackson: I just submitted a PR. Do we need to recompile, or does this happen automatically? Cheers, /E

-- Juan Eugenio Iglesias http://www.jeiglesias.com http://secure-web.cisco.com/1YGjaeYjmBMKwNn_nk2uLZSj_ZFZ-d18GbUHchhXjl9TijuH4aV44-Llrf3dzZPCoFldMuzymtOVDs8KxS-UyR6YhNeVIaz4gI3Ru9WY8PJIF-3e8bOO6gZm8X64C_WDpMP-p_ZtIDMV46z_6vgmupZPygQyB9msvmBhL-mE7anfKm71N7L-MTVv_Nf7NeBKC95zO1vkjhkMvSU8BUXVOSMr2FbqxbXCsUv50VqziA9hrjT3qzoiD9wq7LVjqJuhy547rgrP7Or1bWge4oB6ToRq1SDPNjJAYB1VH6D1gEz1UT0HTFj04tWa3V5Qc-5Pg/http%3A%2F%2Fwww.jeiglesias.com

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 Toms, Robert <Robert.Toms@utdallas.edumailto:Robert.Toms@utdallas.edu> Date: Tuesday, May 13, 2025 at 10:05?AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long

External Email - Use Caution Dear FreeSurfer Community,

I'm longitudinally processing a significant amount of secondary scan data, to get hippocampal subvolumes for a study I'm working on.

Of the hundreds of scans I've processed so far, 18 have failed on line 2136 of SegmentSubfieldsT1Longitudinal.m--a subprocess of the segmentHA_T1_long command-- all with the same final lines:

####### Fitting mesh to image data mask took, at this global iteration and time point, 20.7436 seconds Transforming points Transforming points Wrote image to file image_tp_1.mgz Computing shift introduced by kvlRead Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/mnt/md0/ScratchPad_/ABCD/Package_1234721/image03/derivative/freesurfer/freesurfer8.0.0/NDARINVGCPTFXEV_long/tmp/hippoSF_T1_long.v22_right/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters Unable to perform assignment because the left and right sides have a different number of elements.

Error in SegmentSubfieldsT1Longitudinal (line 2136)

MATLAB:matrix:singleSubscriptNumelMismatch Command exited with non-zero status 249 #######

I've searched the list and no similar errors have been reported. Does anyone know what may be the problem?

I'll attach a couple of the long-hippocampal-subfields.log's in case they can be of help.

FreeSurfer version: 8.0.0

System: Ubuntu 22.04.5 LTS, 512GB RAM

Thanks,

Robert

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Message: 4 Date: Wed, 14 May 2025 06:25:30 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: "Keenlyside, Andrew" <andrew.keenlyside.23@ucl.ac.ukmailto:andrew.keenlyside.23@ucl.ac.uk> Message-ID: <PH0PR04MB8388F2E78E0F58928981D8D5FD96A@PH0PR04MB8388.namprd04.prod.outlook.commailto:PH0PR04MB8388F2E78E0F58928981D8D5FD96A@PH0PR04MB8388.namprd04.prod.outlook.com>

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Dear Matthieu, Which version did you use? The FireANTs version, I presume? Can you please share some screenshots of the incorrect registration? Cheers, /Eugenio

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 Chourrout, Matthieu <m.chourrout@ucl.ac.ukmailto:m.chourrout@ucl.ac.uk> Date: Tuesday, May 13, 2025 at 6:17?AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Keenlyside, Andrew <andrew.keenlyside.23@ucl.ac.ukmailto:andrew.keenlyside.23@ucl.ac.uk> Subject: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?

External Email - Use Caution Hi Freesurfer Community,

The NextBrain page showcases the results of the pipeline on the Edlow brain binned at 200um, but we weren't able to reproduce this on our data with a voxel size < 300 um (thus we binned the data). With my colleague Andrew, we've pinpointed the issue to the cartoon fitting step.

On what system was the NextBrain run at this resolution? I assume it was run on CPU only? Did you have to tweak the cartoon or other key steps to make it run?

Best regards,

Dr Matthieu Chourrout [orcid logo 16px] https://secure-web.cisco.com/1tiMIHDVZbi1_soxzRzk-v66TQ9fs4j0sOPE5nQKOghqmPCbTrhwSaTPfpnxSdARQKbAEQje-REikDuSM16D6HxBsA1I5iTrncEToD4dYzCbGaQ1h6sLrEAe2JH5qGXVFRPTt0Rsrd0GzjSq6OeKZFbx1Mnk6uDnWSQceO2u4Y3nzsoHJGXDVR_swYlewjBAXZ4LRIyQc_MaYR-15E4BOUxHNvWNsKdpWwEz8n4jrstyvGF9vsHwoey9gJql5IQ01-m7GqtoeE4wuXQW--2-akFIN9h3wUzXjOWMfFADRIcAINOllz5_uhx7DsoUGFlk_MFu0D1ooJA8gDP7YHT95V93iNVoq3S0dWOyfyaagjyI/https%3A%2F%2Forcid.org%2F0000-0002-2282-6976

Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural Circuits

UCL Mechanical Engineeringhttps://secure-web.cisco.com/1YgMFScJszy12Gw3eD79ViRNN_Bv5QtTSAxq4Qz7GI7Knh44NLn-kDVVJtKyR7LK94sUplJVxh1lATYUSrER2UAcbZ0P0dDmoQMbwg5HdIOi4c1rnTYKHXSrXmxXbtC3oGEg9jw1AwemQrurolqsKoKPYpgXsO57-c-Rb8bMURDIT1jc5_7tnHNKMjD-8sf5suZ2a9myXU6r4QMFvveB6AfDHk03FbkE8ydQ4n0MPWr-KvWmAs5TmkdjA8Gazo4JkjhAt7o-uAjxDCab7TokSnG95D1CzXwj1w3uhK1b0PJkRpTSQzFyVU15toNEJF3JqWo_ckl9wYaGEMc_0qDkfe6FJVL8O-RsVesFFdr-rDXs/https%3A%2F%2Fwww.ucl.ac.uk%2Fmechanical-engineering%2F

Materials, Structure and Manufacturing at Harwell (MSMaH)https://secure-web.cisco.com/1BkqAWAaOy_nkoRqQ3vWb0R--mjPV-_kDCnT3nqiNmzBSVFsha7kasn-9vaR6PSGrRu6I20ASva5PjyB92Wdk6yYK7vhwA15Az299t1ATK49qrLY2fns-OFklpY1VHQgsm4o3r_NZ4equqKmyMc3nQR3vdD0jY1LsuYTMnAH0vFA4K0L_jetfGWU9RKt9_8tlXCXeMUCGx7GyRG5qLEZTE00VRI5nkEtC_7Tm5rvjpUJcOLinxA5ZcRlbA8S1KHBwp4591NyP6KTKUgvWWj3QxxzpGtE-uVgrWRoDnYk9AVurzoYs81EBA7I3vrfQbcqfWF3lgq41MRhf9ss5Sd8eqgiAIVWcTf874hU5Xj-ff-U/https%3A%2F%2Fwww.ucl.ac.uk%2Fmaterials-harwell%2Fmaterials-structure-and-manufacturing-harwell-activity%23%3A~%3Atext%3DLed%2520by%2520Professor%2520Peter%2520Lee%2Cgroup%2520with%2520over%252030%2520members

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Message: 5 Date: Wed, 14 May 2025 10:36:49 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Subject: Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <4595cecf-781f-4cc5-97dc-e57bdd892a99@mgh.harvard.edumailto:4595cecf-781f-4cc5-97dc-e57bdd892a99@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"

Have you tried using mri_segstats, eg, mri_segstats --seg cerebellum_17_network_${mask_option}_mask.nii.gz --sum cerebellum_17_network_${mask_option}_mask.stats

On 5/8/2025 4:15 AM, Payam Sadeghi Shabestari wrote:

...

????????External Email - Use Caution

Hi FS team,

I'm trying to obtain anatomical statistics for the regions defined in the Choi 2012 and Buckner 2011 parcellations,but I couldn't figure out how to get stats on them. I already did:

for mask_option in "${mask_options[@]}"; do

mri_vol2vol --mov $SUBJECTS_DIR/$subject_id/mri/norm.mgz \

--s $subject_id \

--targ $SUBJECTS_DIR/MNI152/buckner_atlas/17_network_${mask_option}_mask.nii.gz \

--m3z $SUBJECTS_DIR/MNI152/mri/transforms/talairach.m3z \

--noDefM3zPath \

--o $SUBJECTS_DIR/$subject_id/mri/cerebellum_17_network_${mask_option}_mask.nii.gz \

--inv-morph \

--interp nearest

Thank you and best regards, Payam

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Message: 6 Date: Wed, 14 May 2025 17:25:09 +0200 From: Stefano Cerri <ste.45.ste@gmail.commailto:ste.45.ste@gmail.com> Subject: [Freesurfer] Question on Samseg Basic and Samseg for MS lesions To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: LSENNOTT@mgh.harvard.edumailto:LSENNOTT@mgh.harvard.edu Message-ID: <CAC4ov5AcQfx3oXUb=gDL6SK6tcaENkM-ro-F-P50kRgy=LeYTw@mail.gmail.commailto:LeYTw@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi Arianna,

1) Yes. Please note that the method was tuned and mostly tested on MS patients.

2) These two versions of SAMSEG model WMH/ WM lesions differently and cannot be directly compared. The basic SAMSEG is not designed for accurate WMH or WM lesion estimation. Note that you can use the lesion version of SAMSEG on scans without lesions (see Fig. 6 here https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre9ZQKasYmqnwK6bi5vzt5-BaRS02ywgcOcI--IezHyHTAKt807vpLrXUZvO33iKmYOL0EeUkqkVhKXj38poEFY9bY4Djm69SgNrHqC2TpJRpU5OQUybXs5s7nPnXPv0ArkvG_YpXaiip_cs58dLk8TygUTgVuRtW8x9gYHo_BSTpTQs6pwsWwQ2nel-ejGeDe1nkcKTJcqBaT8vZrbLqyVpzVwZRXQDIXUhOjCyNPkbtTJdnT8BSGUjOyXcMp0Etejbfjh9bThJhaEK0tzEhXSLDLIgxCcSmrxk53keXlg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920309563).

3) Yes. Note that SWI data might not add valuable information to the lesion and whole-brain segmentation task. My suggestion is to visually inspect a couple of subjects with and without SWI data.

Stefano

Sent on behalf of Arianna Menardi:

----

Dear Experts,

I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions.

I am new to the approach so I have 3 main questions: 1. Can I use Samseg for MS lesions even if my patients present WM lesions but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images?

Thank you for your help, Arianna

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/1Kb8pmdPdKdYdZdQofh1Zs9Y9vJBM9d8tTBbuN-azPwq2Up... https://secure-web.cisco.com/1tDmFFExvcidAJHTtPomz2TcTR-cmBcLvo3q_epfYYnELlJj_fUE5E2mrg9cDatPEQ-geElCrjJuTaB-qazWOXa5iGBZGLOgpj8pOQP2xaeiKGMTBx0gJLJ7v0j63ezQaAKtr1se2Q3DMPeaMz4eb-wWvG8dFTZuW5tVyAjfVcNFQ--_l8RLrQU0ggiPnC_v6suCGnlD6zxvQ0OURakuse4JLh8gb6PMUJubZMmp2jUneM7KDdD26KmfMDAJzwHmJK0cF0jGYRkc-eaOiWNxVi_rlvwTx1v4BnOH0X2DDI0vtRbTxaUbBooGZawK9XZUCCy5Yyb6piU6khHHqMAPrAg/https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C02%257Cstce%2540di.ku.dk%257Ca91a682c46ca40db5bef08dd929178e4%257Ca3927f91cda14696af898c9f1ceffa91%257C0%257C0%257C638827875690801147%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DZ85vGQiqeULorQXYJrw9WfWWKxixOUCDLs98nEZLA28%253D%26reserved%3D0 .

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Message: 7 Date: Wed, 14 May 2025 17:51:44 +0200 From: Arianna Menardi <arianna.menardi@gmail.commailto:arianna.menardi@gmail.com> Subject: Re: [Freesurfer] Question on Samseg Basic and Samseg for MS lesions To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: LSENNOTT@mgh.harvard.edumailto:LSENNOTT@mgh.harvard.edu Message-ID: <CACojtJJqiYTHZe-M+bgVBcTomvkY8bA59XTSWK6wqAVXkPTwgQ@mail.gmail.commailto:CACojtJJqiYTHZe-M%2BbgVBcTomvkY8bA59XTSWK6wqAVXkPTwgQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Thank you Stefano!

Just an additional curiosity, is there any function within Freesurfer that you think could be used to map and quantify microbleeds in SWI data?

Thanks for the help, Arianna

Il giorno mer 14 mag 2025 alle ore 17:26 Stefano Cerri <ste.45.ste@gmail.commailto:ste.45.ste@gmail.com> ha scritto:

...

    External Email - Use Caution
Hi Arianna,

Yes. Please note that the method was tuned and mostly tested on MS

patients.

These two versions of SAMSEG model WMH/ WM lesions differently and

cannot be directly compared. The basic SAMSEG is not designed for accurate WMH or WM lesion estimation. Note that you can use the lesion version of SAMSEG on scans without lesions (see Fig. 6 here https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre9ZQKasYmqnwK6bi5vzt5-BaRS02ywgcOcI--IezHyHTAKt807vpLrXUZvO33iKmYOL0EeUkqkVhKXj38poEFY9bY4Djm69SgNrHqC2TpJRpU5OQUybXs5s7nPnXPv0ArkvG_YpXaiip_cs58dLk8TygUTgVuRtW8x9gYHo_BSTpTQs6pwsWwQ2nel-ejGeDe1nkcKTJcqBaT8vZrbLqyVpzVwZRXQDIXUhOjCyNPkbtTJdnT8BSGUjOyXcMp0Etejbfjh9bThJhaEK0tzEhXSLDLIgxCcSmrxk53keXlg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920309563 ).

Yes. Note that SWI data might not add valuable information to the

lesion and whole-brain segmentation task. My suggestion is to visually inspect a couple of subjects with and without SWI data.

Stefano

Sent on behalf of Arianna Menardi:

Dear Experts,

I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions.

I am new to the approach so I have 3 main questions:

Can I use Samseg for MS lesions even if my patients present WM lesions

but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images?

Thank you for your help, Arianna

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/1XXzeUVIlswRYB32b4Im8HqpGqypNx3qr57S_8rr-pZADoG... https://secure-web.cisco.com/1tDmFFExvcidAJHTtPomz2TcTR-cmBcLvo3q_epfYYnELlJj_fUE5E2mrg9cDatPEQ-geElCrjJuTaB-qazWOXa5iGBZGLOgpj8pOQP2xaeiKGMTBx0gJLJ7v0j63ezQaAKtr1se2Q3DMPeaMz4eb-wWvG8dFTZuW5tVyAjfVcNFQ--_l8RLrQU0ggiPnC_v6suCGnlD6zxvQ0OURakuse4JLh8gb6PMUJubZMmp2jUneM7KDdD26KmfMDAJzwHmJK0cF0jGYRkc-eaOiWNxVi_rlvwTx1v4BnOH0X2DDI0vtRbTxaUbBooGZawK9XZUCCy5Yyb6piU6khHHqMAPrAg/https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C02%257Cstce%2540di.ku.dk%257Ca91a682c46ca40db5bef08dd929178e4%257Ca3927f91cda14696af898c9f1ceffa91%257C0%257C0%257C638827875690801147%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DZ85vGQiqeULorQXYJrw9WfWWKxixOUCDLs98nEZLA28%253D%26reserved%3D0 .

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Message: 8 Date: Wed, 14 May 2025 15:56:47 +0000 From: Payam Sadeghi Shabestari <payam.sadeghishabestari@uzh.chmailto:payam.sadeghishabestari@uzh.ch> Subject: Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <ZR2P278MB100192423C6AB568E0CBFFB88791A@ZR2P278MB1001.CHEP278.PROD.OUTLOOK.COMmailto:ZR2P278MB100192423C6AB568E0CBFFB88791A@ZR2P278MB1001.CHEP278.PROD.OUTLOOK.COM>

Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

Thanks Douglas, looks like it only returns the whole cerebellum volume (see attached).

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 Douglas N. Greve <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> Date: Wednesday, 14 May 2025 at 16:38 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 Have you tried using mri_segstats, eg, mri_segstats --seg cerebellum_17_network_${mask_option}_mask.nii.gz --sum cerebellum_17_network_${mask_option}_mask.stats

On 5/8/2025 4:15 AM, Payam Sadeghi Shabestari wrote:

External Email - Use Caution Hi FS team, I'm trying to obtain anatomical statistics for the regions defined in the Choi 2012 and Buckner 2011 parcellations, but I couldn't figure out how to get stats on them. I already did: for mask_option in "${mask_options[@]}"; do mri_vol2vol --mov $SUBJECTS_DIR/$subject_id/mri/norm.mgz \ --s $subject_id \ --targ $SUBJECTS_DIR/MNI152/buckner_atlas/17_network_${mask_option}_mask.nii.gz \ --m3z $SUBJECTS_DIR/MNI152/mri/transforms/talairach.m3z \ --noDefM3zPath \ --o $SUBJECTS_DIR/$subject_id/mri/cerebellum_17_network_${mask_option}_mask.nii.gz \ --inv-morph \ --interp nearest Thank you and best regards, Payam

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Message: 9 Date: Wed, 14 May 2025 16:10:02 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? To: "Keenlyside, Andrew" <andrew.keenlyside.23@ucl.ac.ukmailto:andrew.keenlyside.23@ucl.ac.uk>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <PH0PR04MB838817DF66D15AD24BC834C6FD91A@PH0PR04MB8388.namprd04.prod.outlook.commailto:PH0PR04MB838817DF66D15AD24BC834C6FD91A@PH0PR04MB8388.namprd04.prod.outlook.com>

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Oooohhhh I see. Yeah you?ll have to run in CPU mode on a machine with quite a lot of RAM ?

From: Keenlyside, Andrew <andrew.keenlyside.23@ucl.ac.ukmailto:andrew.keenlyside.23@ucl.ac.uk> Date: Wednesday, May 14, 2025 at 3:27?AM To: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?

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Dear Juan,

This was run with the fast version of NextBrain using the CPU running on a 313um HiP-CT scan of the brain (29MB). The GPU version at this resolution failed when I was trying to run it on a fairly large workstation (A1000 GPU ~48GB VRAM)

The issue is not quite the performance of the model at ~300um, we have issues with the running of a 150um scan which is killed during the fitting step.

We were wondering which versions you used to get the 150um segmentation of the edlow et al. MRI brain? And if you have any advice which might help us here,

Kind regards, Andrew

Andrew Keenlyside PhD Student, UCL Mech. Eng. ________________________________ From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Sent: 14 May 2025 07:25 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Keenlyside, Andrew <andrew.keenlyside.23@ucl.ac.ukmailto:andrew.keenlyside.23@ucl.ac.uk> Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?

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Dear Matthieu,

Which version did you use? The FireANTs version, I presume?

Can you please share some screenshots of the incorrect registration?

Cheers,

/Eugenio

Juan Eugenio Iglesias

http://www.jeiglesias.com http://secure-web.cisco.com/1YGjaeYjmBMKwNn_nk2uLZSj_ZFZ-d18GbUHchhXjl9TijuH4aV44-Llrf3dzZPCoFldMuzymtOVDs8KxS-UyR6YhNeVIaz4gI3Ru9WY8PJIF-3e8bOO6gZm8X64C_WDpMP-p_ZtIDMV46z_6vgmupZPygQyB9msvmBhL-mE7anfKm71N7L-MTVv_Nf7NeBKC95zO1vkjhkMvSU8BUXVOSMr2FbqxbXCsUv50VqziA9hrjT3qzoiD9wq7LVjqJuhy547rgrP7Or1bWge4oB6ToRq1SDPNjJAYB1VH6D1gEz1UT0HTFj04tWa3V5Qc-5Pg/http%3A%2F%2Fwww.jeiglesias.com

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 Chourrout, Matthieu <m.chourrout@ucl.ac.ukmailto:m.chourrout@ucl.ac.uk> Date: Tuesday, May 13, 2025 at 6:17?AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Keenlyside, Andrew <andrew.keenlyside.23@ucl.ac.ukmailto:andrew.keenlyside.23@ucl.ac.uk> Subject: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?

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Hi Freesurfer Community,

On what system was the NextBrain run at this resolution? I assume it was run on CPU only? Did you have to tweak the cartoon or other key steps to make it run?

Best regards,

Dr Matthieu Chourrout [Image removed by sender. orcid logo 16px] https://secure-web.cisco.com/1tiMIHDVZbi1_soxzRzk-v66TQ9fs4j0sOPE5nQKOghqmPCbTrhwSaTPfpnxSdARQKbAEQje-REikDuSM16D6HxBsA1I5iTrncEToD4dYzCbGaQ1h6sLrEAe2JH5qGXVFRPTt0Rsrd0GzjSq6OeKZFbx1Mnk6uDnWSQceO2u4Y3nzsoHJGXDVR_swYlewjBAXZ4LRIyQc_MaYR-15E4BOUxHNvWNsKdpWwEz8n4jrstyvGF9vsHwoey9gJql5IQ01-m7GqtoeE4wuXQW--2-akFIN9h3wUzXjOWMfFADRIcAINOllz5_uhx7DsoUGFlk_MFu0D1ooJA8gDP7YHT95V93iNVoq3S0dWOyfyaagjyI/https%3A%2F%2Forcid.org%2F0000-0002-2282-6976

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Message: 10 Date: Wed, 14 May 2025 16:18:05 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Subject: Re: [Freesurfer] SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are disorganized volumes usable? To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <PH0PR04MB8388AD78A13D63ACECB468B6FD91A@PH0PR04MB8388.namprd04.prod.outlook.commailto:PH0PR04MB8388AD78A13D63ACECB468B6FD91A@PH0PR04MB8388.namprd04.prod.outlook.com>

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Dear Robert, Sorry for the slow response. Yes, it should be fine. Cheers, /Eugenio

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 Toms, Robert <Robert.Toms@utdallas.edumailto:Robert.Toms@utdallas.edu> Date: Monday, May 5, 2025 at 1:00?PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are disorganized volumes usable?

External Email - Use Caution (please see below) ________________________________ From: Toms, Robert Sent: Monday, May 5, 2025 2:55 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: SegmentSubfieldsT1Longitudinal Error, Line 2136 -- Are disorganized volumes usable?

Dear Experts,

I'm having the same error as this 2023 post that y'all responded to: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74833.html https://secure-web.cisco.com/1KLNWDehAqxG8KDuAFS_PiyAmb7ReDrlW1jhYv0TnF48GSndSak63itMGb9sVmiGsGYcdrHdu0oBotS68zPtzY8AB2pCamXIYZ7FjLyKfkKhF0kL-KiBT3KAsxUaA7njaLqOpftYMe1gy9UjlU6caLO8M42ytsOcSH5B6Ks9Wqf7ah2KvcpwXh3rEi-R4dUF8RAbU0tnEug1ymjaoBgwst0ZiTbXJyL4iG_FRv-KYoQ3zxXe7BzfS6tVRwy1rfg8xW8b0lbYIzJ7mt6sbtLTzAdxU90A7G2c6VuUYULAmIEOO_WkjBOxL-6OMQ13vD5iZ8dF3ZPilBhutekznO1a7xg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74833.html https://secure-web.cisco.com/15Vt3zMobf7Y4tHpCjLxvyPhoC2gjNR1_ZY3GyZjqm3L4sTIpRNxmYobtpX8i9ixxWYSwuCiHkfWl7Taj_Qcjd5hwAH_rJA8UMd3bEzs87cjEQD1QiiaHA1aBbUEamu_jQ76ce_5wbkfCOeDKGX92oQb0UuBBPILreVMRcdZFFRSX2V6kvuG6F1ElzZooIk-mZUblmT3x5Hs73aSc3NYssK7rUSmWFIxrvJpQPO3M2nbqIZaaA2jtn7dl-QOr0zh437aPYtD7KmRyEi8aihdyfZUJXHrP5gPZfjjV7IFZ5DCLwYFPmh889djjddsR6ORv0CM13ZKyHRaa2QczU0MJAg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74833.html

I'm running FreeSurfer 8.0.0 on Ubuntu 22.04.5 LTS, and most of my subjects have run through the whole pipeline with no problems.

You told the original 2023 poster that the 2 timepoint volumes are disorganized, but still usable?which was very helpful, and covers most of my error cases, however two of my errored-out subjects have 3 timepoints. I wanted to check with you in case 3-timepoint volumes wouldn't be usable for some reason?

The following volumes are in base/tmp/hippoSF_T1_long.v22_right/ : volumesAmygdala_tp_1.txt volumesAmygdala_tp_2.txt volumesAmygdala_tp_3.txt volumesHippo_tp_1.txt volumesHippo_tp_2.txt volumesHippo_tp_3.txt

I've attached the logs for both of them, and the final lines of both logs are identical:

Applying LTAtransformInterp (resample_type 0) writing to discreteLabelsMergedBodyHeadNoMLorGCDGResampledT1_tp_2.mgz... Transforming points Transforming points Wrote image to file image_tp_3.mgz This file does not contain MRI parameters Unable to perform assignment because the left and right sides have a different number of elements.

Error in SegmentSubfieldsT1Longitudinal (line 2136)

Thank you! Robert

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Message: 11 Date: Wed, 14 May 2025 17:13:51 +0000 From: "Nolan, Jackson" <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long To: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB66705B95651DC11363D8F194AB91A@MN2PR04MB6670.namprd04.prod.outlook.commailto:MN2PR04MB66705B95651DC11363D8F194AB91A@MN2PR04MB6670.namprd04.prod.outlook.com>

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Hey Eugenio,

Unfortunately, this will require a recompile of the tool. None of the Matlab executables are compiled during the build, as this requires a full Matlab license, which we do not want to be a prerequisite to run FS.

Happy to help get the new version rebuild, I?ll just need to confirm with Rob exactly what needs to be supported.

Best, Jackson

From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Date: Wednesday, May 14, 2025 at 2:25?AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Nolan, Jackson <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu> Subject: Re: Hippocampal Subvolumes Error -- segmentHA_T1_long Thanks for catching this, Robert. It?s a small bug that does not affect the results on the cases that didn?t crash. Jackson: I just submitted a PR. Do we need to recompile, or does this happen automatically? Cheers, /E

External Email - Use Caution Dear FreeSurfer Community,

I'm longitudinally processing a significant amount of secondary scan data, to get hippocampal subvolumes for a study I'm working on.

Of the hundreds of scans I've processed so far, 18 have failed on line 2136 of SegmentSubfieldsT1Longitudinal.m--a subprocess of the segmentHA_T1_long command-- all with the same final lines:

Error in SegmentSubfieldsT1Longitudinal (line 2136)

MATLAB:matrix:singleSubscriptNumelMismatch Command exited with non-zero status 249 #######

I've searched the list and no similar errors have been reported. Does anyone know what may be the problem?

I'll attach a couple of the long-hippocampal-subfields.log's in case they can be of help.

FreeSurfer version: 8.0.0

System: Ubuntu 22.04.5 LTS, 512GB RAM

Thanks,

Robert

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Message: 12 Date: Wed, 14 May 2025 19:33:16 +0000 From: "Toms, Robert" <Robert.Toms@utdallas.edumailto:Robert.Toms@utdallas.edu> Subject: Re: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long To: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <BN0PR01MB6959746A36B61A1F19E4D1478191A@BN0PR01MB6959.prod.exchangelabs.commailto:BN0PR01MB6959746A36B61A1F19E4D1478191A@BN0PR01MB6959.prod.exchangelabs.com>

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Dear Eugenio and Jackson,

Thanks for your help! Can you confirm that the output is accurate?

For context, we'll be processing >14,000 subjects' longitudinal data on our university's HPC cluster (so at this rate we may end up with 300+ with the same problem), and we have a full matlab license. If there is a way to recompile and have these not error out, please let me know!

Thanks, Robert ________________________________ 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 Nolan, Jackson <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu> Sent: Wednesday, May 14, 2025 12:13 PM To: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long

Hey Eugenio,

Unfortunately, this will require a recompile of the tool.

None of the Matlab executables are compiled during the build, as this requires a full Matlab license, which we do not want to be a prerequisite to run FS.

Happy to help get the new version rebuild, I?ll just need to confirm with Rob exactly what needs to be supported.

Best,

Jackson

Cheers,

Juan Eugenio Iglesias

http://secure-web.cisco.com/1fSpKx_yH2lsd2KxtoXU-3auXZ5elj-ZWEct3DmzXAJ4QFoy...

External Email - Use Caution

Dear FreeSurfer Community,

I'm longitudinally processing a significant amount of secondary scan data, to get hippocampal subvolumes for a study I'm working on.

Of the hundreds of scans I've processed so far, 18 have failed on line 2136 of SegmentSubfieldsT1Longitudinal.m--a subprocess of the segmentHA_T1_long command-- all with the same final lines:

#######

Fitting mesh to image data mask took, at this global iteration and time point, 20.7436 seconds

Transforming points

Wrote image to file image_tp_1.mgz

Computing shift introduced by kvlRead

Constructing image-to-world transform from header information (asmr1.mgz)

Constructing image-to-world transform from header information (/mnt/md0/ScratchPad_/ABCD/Package_1234721/image03/derivative/freesurfer/freesurfer8.0.0/NDARINVGCPTFXEV_long/tmp/hippoSF_T1_long.v22_right/imageDump.mgz)

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

Unable to perform assignment because the left and right sides have a different number of elements.

Error in SegmentSubfieldsT1Longitudinal (line 2136)

MATLAB:matrix:singleSubscriptNumelMismatch

Command exited with non-zero status 249

#######

I've searched the list and no similar errors have been reported. Does anyone know what may be the problem?

I'll attach a couple of the long-hippocampal-subfields.log's in case they can be of help.

FreeSurfer version: 8.0.0

System: Ubuntu 22.04.5 LTS, 512GB RAM

Thanks,

Robert

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------------------------------

Message: 13 Date: Wed, 14 May 2025 18:37:17 -0400 From: Gonzalo Rojas Costa <gonzalo.rojas.costa@gmail.commailto:gonzalo.rojas.costa@gmail.com> Subject: [Freesurfer] mri segstats "masksign abs" syntaxis option To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <CAHPHMw4MQh1wjuA6_yUNy_cmpNDQ383zf9YYKnMDcbh6MVNTjQ@mail.gmail.commailto:CAHPHMw4MQh1wjuA6_yUNy_cmpNDQ383zf9YYKnMDcbh6MVNTjQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi:

Using "--masksign abs" option: which must be the syntax for "--maskthresh" option in mri_segstats command?

Sincerely,

Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University Santiago Chile -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20250514/bf...http://secure-web.cisco.com/1CaS23ub7ilYB0R0-VyKNyhAkwfKT7_Chk3XmpqvBH6FMzEVYQl-86y1avNDpSce1G-AyWKaw6Le7upf7wRyXzzd-OCcfsVZPu3qy56ZwehjJ44V0AeE4FbvDo8J-0KHX0lH-Q3xElEFcNfOGgJkzRrNZB-3U2-l_9DVPywASDeyASOgt4ZjoDVUZGWS24WLOgqQNx_cvFP1oCDZ5d-uk-khbOm5rlhipJErGWeIy6GVqluDCDUsV2UFnLZPqVLE8u94X1tNNOE_V5qSPjCu83g6iU9GDlW0sjTBFsaW2lb_7Rn6mvChQUJCBQxCuBp7Ij_U6BN34IJgHMBlHXbtC7Q/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250514%2Fbfff0fd1%2Fattachment-0001.html

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Message: 14 Date: Wed, 14 May 2025 23:07:59 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subvolumes Error -- segmentHA_T1_long To: "Toms, Robert" <Robert.Toms@UTDallas.edumailto:Robert.Toms@UTDallas.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <PH0PR04MB838852D0CE7EBBD68E317E3CFD91A@PH0PR04MB8388.namprd04.prod.outlook.commailto:PH0PR04MB838852D0CE7EBBD68E317E3CFD91A@PH0PR04MB8388.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Yeah the plan is to fix, recompile, and distribute the fix

From: Toms, Robert <Robert.Toms@UTDallas.edumailto:Robert.Toms@UTDallas.edu> Date: Wednesday, May 14, 2025 at 12:33?PM To: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: Hippocampal Subvolumes Error -- segmentHA_T1_long

External Email - Use Caution Dear Eugenio and Jackson,

Thanks for your help! Can you confirm that the output is accurate?

Hey Eugenio,

Unfortunately, this will require a recompile of the tool.

None of the Matlab executables are compiled during the build, as this requires a full Matlab license, which we do not want to be a prerequisite to run FS.

Happy to help get the new version rebuild, I?ll just need to confirm with Rob exactly what needs to be supported.

Best,

Jackson

Cheers,

Juan Eugenio Iglesias

External Email - Use Caution

Dear FreeSurfer Community,

I'm longitudinally processing a significant amount of secondary scan data, to get hippocampal subvolumes for a study I'm working on.

Of the hundreds of scans I've processed so far, 18 have failed on line 2136 of SegmentSubfieldsT1Longitudinal.m--a subprocess of the segmentHA_T1_long command-- all with the same final lines:

#######

Fitting mesh to image data mask took, at this global iteration and time point, 20.7436 seconds

Transforming points

Wrote image to file image_tp_1.mgz

Computing shift introduced by kvlRead

Constructing image-to-world transform from header information (asmr1.mgz)

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

Unable to perform assignment because the left and right sides have a different number of elements.

Error in SegmentSubfieldsT1Longitudinal (line 2136)

MATLAB:matrix:singleSubscriptNumelMismatch

Command exited with non-zero status 249

#######

I've searched the list and no similar errors have been reported. Does anyone know what may be the problem?

I'll attach a couple of the long-hippocampal-subfields.log's in case they can be of help.

FreeSurfer version: 8.0.0

System: Ubuntu 22.04.5 LTS, 512GB RAM

Thanks,

Robert

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------------------------------

Message: 15 Date: Thu, 15 May 2025 10:07:39 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Subject: Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <da7fdb15-d537-4c4a-aa69-ea0a4dfd1d6b@mgh.harvard.edumailto:da7fdb15-d537-4c4a-aa69-ea0a4dfd1d6b@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"

Two things to check 1. Look at the image and make sure it has all the segs you expect, if, so 2. You may need to give mri_segstats a color table like $FREESURFER/FreeSurferColorLUT.txt. Does the Choi atlas come with one? You can pass it with --ctab colortab.txt

On 5/14/2025 11:56 AM, Payam Sadeghi Shabestari wrote:

...

????????External Email - Use Caution

Thanks Douglas, looks like it only returns the whole cerebellum volume (see attached).

*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 Douglas N. Greve <dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU> *Date: *Wednesday, 14 May 2025 at 16:38 *To: *freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011

Have you tried using mri_segstats, eg, mri_segstats --seg cerebellum_17_network_${mask_option}_mask.nii.gz --sum cerebellum_17_network_${mask_option}_mask.stats

On 5/8/2025 4:15 AM, Payam Sadeghi Shabestari wrote:
*????????External Email - Use Caution *

Hi FS team,

I'm trying to obtain anatomical statistics for the regions defined
in the Choi 2012 and Buckner 2011 parcellations, but I couldn't
figure out how to get stats on them. I already did:

for mask_option in "${mask_options[@]}"; do

mri_vol2vol --mov $SUBJECTS_DIR/$subject_id/mri/norm.mgz \

--s $subject_id \

--targ
$SUBJECTS_DIR/MNI152/buckner_atlas/17_network_${mask_option}_mask.nii.gz
\

--m3z $SUBJECTS_DIR/MNI152/mri/transforms/talairach.m3z \

--noDefM3zPath \

--o
$SUBJECTS_DIR/$subject_id/mri/cerebellum_17_network_${mask_option}_mask.nii.gz
\

--inv-morph \

--interp nearest

Thank you and best regards,
Payam



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------------------------------

Message: 16 Date: Thu, 15 May 2025 10:08:00 -0400 From: "Douglas N. Greve" <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Subject: Re: [Freesurfer] Question on Samseg Basic and Samseg for MS lesions To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <f16a02e1-7d3b-4ce6-9ec9-1293cedc5dab@mgh.harvard.edumailto:f16a02e1-7d3b-4ce6-9ec9-1293cedc5dab@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"

No, I don't think so.

On 5/14/2025 11:51 AM, Arianna Menardi wrote:

...

????????External Email - Use Caution

Thank you Stefano!

Just an additional curiosity, is there any function within Freesurfer that you think could be used to map and quantify microbleeds in SWI data?

Thanks for the help, Arianna

Il giorno mer 14 mag 2025 alle ore 17:26 Stefano Cerri <ste.45.ste@gmail.commailto:ste.45.ste@gmail.com> ha scritto:

????????External Email - Use Caution

Hi Arianna,

1) Yes. Please note that the method was tuned and mostly tested on
MS patients.

2) These two versions of SAMSEG?model WMH/ WM?lesions differently
and cannot be directly compared. The basic SAMSEG is not designed
for accurate WMH or WM lesion estimation. Note that you can use
the lesion version of SAMSEG on scans without lesions (see Fig. 6
here
<https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre9ZQKasYmqnwK6bi5vzt5-BaRS02ywgcOcI--IezHyHTAKt807vpLrXUZvO33iKmYOL0EeUkqkVhKXj38poEFY9bY4Djm69SgNrHqC2TpJRpU5OQUybXs5s7nPnXPv0ArkvG_YpXaiip_cs58dLk8TygUTgVuRtW8x9gYHo_BSTpTQs6pwsWwQ2nel-ejGeDe1nkcKTJcqBaT8vZrbLqyVpzVwZRXQDIXUhOjCyNPkbtTJdnT8BSGUjOyXcMp0Etejbfjh9bThJhaEK0tzEhXSLDLIgxCcSmrxk53keXlg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920309563>).

3) Yes. Note that?SWI data might not add valuable?information to
the lesion and whole-brain segmentation task. My suggestion is to
visually inspect a couple of subjects with and without SWI data.

Stefano

Sent on behalf of Arianna Menardi:
----
Dear Experts,
I'm trying to quantify the volume of some white matter lesions in
an elderly group. I have tried using both Samseg cross-sectional,
as well as Samseg for MS lesions.
I am new to the approach so I have 3 main questions:
1. Can I use Samseg for MS lesions even if my patients present WM
lesions but are not MS patients?
2. the estimated values of WM-hypointensities derived from the
basic version of Samseg are almost half in size compared to the
output 'Lesions" of Samseg specific for MS lesions. What is hence
the difference between the two approaches that could explain such
a big difference in the output?
3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the
algorithms are not suited for SWI images?
Thank you for your help,
Arianna
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Ania Holubecki
Wang, Ruopeng