Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
Thanks, Franziska. It seems to be a problem with partial voluming. Cerebral white matter (white pixels) mixes with a thin layer of cerebrospinal fluid (black pixels) and the result is a bunch of gray pixels that look like the pulvinar. Partial voluming is one of the biggest problems with these Bayesian segmentation methods, the price you pay for the (huge!) advantage of being agnostic to / robust against changes in MR contrast of the input scan... Unfortunately, there is no easy fix for this at the moment. Normally, the increment in volume due to the leak is not as large as it may seem because segmentations are weighted by their probabilities when computing volumes. In the future, we plan to tackle this with deep learning methods that do a fantastic job with partial voluming. The problems with this approach are: 1. Robustness against contrast changes, and (mostly) 2. Training with ex vivo data is tricky. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 3/16/21, 03:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gronow, Franziska" wrote: External Email - Use Caution Dear Eugenio, here are the zipped norm.mgz and automated segmentations for two subjects: https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7D74Z2Par77m2PVo3Wm0nQOKU_ZQ-VZllAjpGFcJ7zfC7AlgdlnICsp__aPb0nZFYLze4Y4r4hXIerT0tQVso_xsDOOgtYVy_dklam9cgKMC-wR52zgKm5jglckTj8HXlBbyMSOoPV9vsz-z-JKtmPpLDPR8TNqyWG8oqsdSGX66xfPZQlqhlzyTmUwm1X5mSPeKecX9Fn3hcELI917WBy-1yix24jyDIneXrAWikw/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2FmzyagMpXgSmDbBo Hope this helps! Best regards, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
External Email - Use Caution Dear Eugenio, here are the zipped norm.mgz and automated segmentations for two subjects: https://secure-web.cisco.com/1NFOUrkRWZ6w5iEt9PtCxQNkjFZr9fIybWKJt1Rx3T_PB7D74Z2Par77m2PVo3Wm0nQOKU_ZQ-VZllAjpGFcJ7zfC7AlgdlnICsp__aPb0nZFYLze4Y4r4hXIerT0tQVso_xsDOOgtYVy_dklam9cgKMC-wR52zgKm5jglckTj8HXlBbyMSOoPV9vsz-z-JKtmPpLDPR8TNqyWG8oqsdSGX66xfPZQlqhlzyTmUwm1X5mSPeKecX9Fn3hcELI917WBy-1yix24jyDIneXrAWikw/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2FmzyagMpXgSmDbBo Hope this helps! Best regards, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
Yes! Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 3/15/21, 08:36, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gronow, Franziska" wrote: External Email - Use Caution Dear Eugenio, do you mean the "ThalamicNuclei.v12.T1.mgz" files? Best regards, Franziska ___ Date: Thu, 11 Mar 2021 16:29:45 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list Dear Franziska, Can you please send the automated segmentations as well? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/141gcV3WY5mJIjV2uPDoq59J1j9A_zAepv_kVvEZA1jJ2mug1lkKUR5yoNaV6M0Zvtnhm3gn8yGPte_48BoO-JY_QrAoYKxlRIfkeXmYIEcdX4WSVWH2lkt3PB1C-RCyoDubggQQar_L6e5QVO_uEBOW_PyBz-3vdxwVmZwrB3FwyKaUm1BhjG90py57Ra29h_B3dzUBGPuWAXQXkdTFhTENSfFdEnYreP9UDacODv9LSjxJkwI2PSPmwCk58JnMYDvXE10_Gcr1R52k6POOK6g/http%3A%2F%2Fwww.jeiglesias.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
External Email - Use Caution Dear Eugenio, do you mean the "ThalamicNuclei.v12.T1.mgz" files? Best regards, Franziska ___ Date: Thu, 11 Mar 2021 16:29:45 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list Dear Franziska, Can you please send the automated segmentations as well? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/141gcV3WY5mJIjV2uPDoq59J1j9A_zAepv_kVvEZA1jJ2mug1lkKUR5yoNaV6M0Zvtnhm3gn8yGPte_48BoO-JY_QrAoYKxlRIfkeXmYIEcdX4WSVWH2lkt3PB1C-RCyoDubggQQar_L6e5QVO_uEBOW_PyBz-3vdxwVmZwrB3FwyKaUm1BhjG90py57Ra29h_B3dzUBGPuWAXQXkdTFhTENSfFdEnYreP9UDacODv9LSjxJkwI2PSPmwCk58JnMYDvXE10_Gcr1R52k6POOK6g/http%3A%2F%2Fwww.jeiglesias.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
Dear Franziska, Can you please send the automated segmentations as well? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 3/11/21, 09:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gronow, Franziska" wrote: External Email - Use Caution Here are the norm.mgz files of two subjects as .zip file: https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzIdjkIjTOvtomItfqHsdtu1RXIan9sqawThsD1AInX2PV_jNS-9gp_FPgvgzSNu5cvTJ3FuX_AJhQoY7ADXl3WDZ7EypfhlOS6dgCV2hdRIEtwFUpEFgZxu8x62DXJzDHVEYp5Edr22tcIE79zGpIu-qXANDWaexYIMUXA9XJvYhyCYYfcsyIlXrXQk9MkoF3_ONddEpAyG3iOnx4ErXzREE-nIZebs_59EE0Bp7Kgg/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2Fz53CsHgjz7rC2zj Thanks for your help! Best regards, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
External Email - Use Caution Here are the norm.mgz files of two subjects as .zip file: https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzIdjkIjTOvtomItfqHsdtu1RXIan9sqawThsD1AInX2PV_jNS-9gp_FPgvgzSNu5cvTJ3FuX_AJhQoY7ADXl3WDZ7EypfhlOS6dgCV2hdRIEtwFUpEFgZxu8x62DXJzDHVEYp5Edr22tcIE79zGpIu-qXANDWaexYIMUXA9XJvYhyCYYfcsyIlXrXQk9MkoF3_ONddEpAyG3iOnx4ErXzREE-nIZebs_59EE0Bp7Kgg/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2Fz53CsHgjz7rC2zj Thanks for your help! Best regards, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
Dropbox is fine. Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Gronow, Franziska" Reply-To: Freesurfer support list Date: Wednesday, March 10, 2021 at 05:31 To: "'freesurfer@nmr.mgh.harvard.edu'" Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? External Email - Use Caution Dear Eugenio, thanks for your response. I wasn’t sure whether .mgz files contain patient information so I had to clarify that. It would be great if you could take a look on the affected cases. I could send you norm.mgz files of one or more subjects. Can I send them directly via email or do you prefer dropbox? Thanks again! Best regards, Franziska -- Message: 17 Date: Tue, 23 Feb 2021 16:20:43 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list Message-ID: <1f81bc20-3ba0-4a5b-b507-13eed2bee...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sure! The more slices the better __ Maybe it would be possible to share norm.mgz (which is skull stripped and thus deidentified) and the segmentation? Or maybe even crop norm.mgz around the thalami with Freeview? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com ?On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gronow, Franziska" wrote: External Email - Use Caution Dear Eugenio, thank you for your response. Unfortunately it is not possible to share the whole subject. Would it be helpful to send you more screenshots of all three views (coronal, sagittal, axial) with different mask opacities? Kind regards, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
External Email - Use Caution Dear Eugenio, thanks for your response. I wasn't sure whether .mgz files contain patient information so I had to clarify that. It would be great if you could take a look on the affected cases. I could send you norm.mgz files of one or more subjects. Can I send them directly via email or do you prefer dropbox? Thanks again! Best regards, Franziska -- Message: 17 Date: Tue, 23 Feb 2021 16:20:43 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list Message-ID: <1f81bc20-3ba0-4a5b-b507-13eed2bee...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sure! The more slices the better __ Maybe it would be possible to share norm.mgz (which is skull stripped and thus deidentified) and the segmentation? Or maybe even crop norm.mgz around the thalami with Freeview? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/11XaMU-QoiZKnXiNuQPJicEtr4gYDxjHq1ZrbybgK3HfB2JNtRZNtkp7LR4JPl6-pJz7sJHs8M-kH8Ci1A2-q8tJMtyChK6Wqv1wSkgzw8cY2K8Au4uGqJYiUxurISKRuzojPPxghTgD1R_HeBZly0U4i-PoeTS1vwrz2qscnBKCg5bK0kZFv8yRqQgUqkhE0YMCxqMENl9178aKiHu_OjKnJ4r1DFuB193GIpdgcoVjT8aVsbV7dt5DelQ47g1joONClSugcb-lAudzsb0y5lQ/http%3A%2F%2Fwww.jeiglesias.com ?On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gronow, Franziska" wrote: External Email - Use Caution Dear Eugenio, thank you for your response. Unfortunately it is not possible to share the whole subject. Would it be helpful to send you more screenshots of all three views (coronal, sagittal, axial) with different mask opacities? Kind regards, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
; > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc > pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q > nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN > FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE > 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer -- next part -- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1JvBfmBi57GPnae3pffFHMt7spN6t92V5q1T0KcXFfz112mLbY18bi4zNYqaR1fDllzuPRzvHPPZdhJsFy_-JS_5TYCypyTd1DV0gQJ81Vnbun-w1jgpS-nfAm_-xzKpU5Ahvz3D6YuiiBxYVQnnu9El0ohZ5YagIdqXdrc43RZCrThc2UylfmrcEP886ol_DPKenpIizoowtawtzz6jO51KKU2At0huy5rSrNZVc1NMkBOVtnBiLJO4aMh4DTDzbg8Wyv80_vcz45LmZe01n8g/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210216%2Fd3f31b14%2Fattachment-0001.html -- Message: 3 Date: Wed, 17 Feb 2021 17:36:49 +0900 From: ? Subject: [Freesurfer] VB password To: freesurfer@nmr.mgh.harvard.edu Message-ID: <3888b0f5-515a-4637-83f6-38e635234...@fmu.ac.jp> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am attempting to run the Freesurfer Ubuntu virtual box but I need the ?Developed? password. Is it possible to have it? Best Mudathir -- Message: 4 Date: Wed, 17 Feb 2021 08:54:00 + From: "Gronow, Franziska" Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: "'freesurfer@nmr.mgh.harvard.edu'" Message-ID: Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear Freesurfer experts, I've been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the "Segmentation of thalamic nuclei" tool by Iglesias, J.E. et al. The "recon-all" as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases - regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://secure-web.cisco.com/13NyoIuwpnsiHWemQxkjh3X8nFYXTG9wpVXrDAWJsCjxurFVaijSCi6HJ1omS-JnHaipqYf5OTTQWIpbyRGx1_9uZDcFhQbX6Iz_gAK-PbGYNDeH6sLSwTH44gEtwTIIDN3jA24q3bDrmmkiYMtKoLeNzHyjPGySb1cHLbldpyoJgJe3zdizx9tlVc9dPMmRMk-DDBSBpmAmCPpY0ZiHiy612_W6DLESWA4wfED2Qh1qBp1OOpbisCCSiSBzrCY031mQMzsBKD7lNrvAIk8bVHA/https%3A%2F%2Fwww.dropbox.com%2Fsh%2F53fhanytrt4es6e%2FAAAqEmgl7N5YqpxDYMfxHQDAa%3Fdl%3D0 Thanks for your help! Best, Franziska -- next part -- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1ECNXWqO94EJVZVeb7iMk1BsG9wi8gwFIWYvEzard63w21fdaGW_NDodTLY-1zMq7uVsE34ivcNnpQPvd8VqdhLmd1u--Q7A_8xeM5zUiwnSBFHJiUdXnQzmxjP4YR-2aytn6piJt9nZwMSTcvqrIWDdDOhR96I7bryAgX6o_Gg-NRIIZ38qyUHPCnuqwX7PskHO7s9771CxNdI-1pZdVbQlwNQschoYBNYYrKn1Ph7By_554GxB2_G36fnm8wwv2Wo4P_OylJ61xyiTmnqbMlg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210217%2F08e84db1%2Fattachment-0001.html -- Message: 5 Date: Wed, 17 Feb 2021 14:57:46 +0530 From: Koustav Chatterjee Subject: [Freesurfer] Queries in qdec To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Forum members, May I get your help please to resolve 2 queries below? 1. I am unable to see .tiff files taken through 'quicksnaps.tiff' of the 'qdec' analysed data. Even after completing the process of 'quicksnaps.tiff' successfully, I can see only black screen while opening the file. Please find a sample pic of how those files look. [image: image.png] 2. I am using FreeSurfer version 6 where I am *missing 'Design Matrix Type'* inside the 'design' tab of 'qdec' command. [image: image.png] Thank you for your time and help. Regard
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
e, but processed with > FS7.1.1, resulting in 147,292 vertices and 294,580 faces. > > > > > > I have run this on several T1 files with similar results on each. > FreeSurfer 6 surfaces always look smooth and refract light nicely. > FreeSurfer 7 surfaces do not. I'm out of ideas, and the only > difference I can find is FreeSurfer version, so thank you to anyone > who can point me in the right direction to fix this issue. > > > > Mike Schmidt > > > > ___ > > 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/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc > pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q > nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN > FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE > 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/151XcoRtTQC4OuyWsUg_M6YaqNPU7-BFePkTz9D3 > 8voAw2SojRuKp89ghg0dzi01RYRhFLrN-_3pB2qdbYbKVLOIuyP8NeraHvXZ-9sXtxFK2I > m5NG3kq2YDEpP_g7vgJlTq3ZQz3Tih5usiHtKApz0p9-BD-4o0ukbnCvJc2TvUjqya33Hw > n4wwgF1mF_LnFJHqZ1LESxIGJoSKXKWe9x9Vu3D1Ak7WDRc6ED8E9yGj3mACdRHGybBiK6 > 0Sv6zZaqCBZMeTEveLMGvvH49PyFA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2 > Fmailman%2Flistinfo%2Ffreesurfer> > > > > ___ > 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/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc > pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q > nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN > FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE > 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/151XcoRtTQC4OuyWsUg_M6YaqNPU7-BFePkTz9D3 > 8voAw2SojRuKp89ghg0dzi01RYRhFLrN-_3pB2qdbYbKVLOIuyP8NeraHvXZ-9sXtxFK2I > m5NG3kq2YDEpP_g7vgJlTq3ZQz3Tih5usiHtKApz0p9-BD-4o0ukbnCvJc2TvUjqya33Hw > n4wwgF1mF_LnFJHqZ1LESxIGJoSKXKWe9x9Vu3D1Ak7WDRc6ED8E9yGj3mACdRHGybBiK6 > 0Sv6zZaqCBZMeTEveLMGvvH49PyFA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2 > Fmailman%2Flistinfo%2Ffreesurfer> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc > pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q > nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN > FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE > 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1SgV2glVuOyoBdsfxbWPmyTT48xKmRwmuYy9Jvcfc > pCVCI1eDxPv7zs20HCE1pSgRa32-GxhOugribbC4x-1DRaQ4HK4MYwfVKSp8ORpyNBvC6q > nvTvYo6d5KAHMA2is3GnVbEPv6BQg56jD8J9kSjBqYaA9xjm2eNhXSNfbZp9TadwOK4pjN > FHKQleraeg4R4NiZo5ziNr8rY1dU_xbyoTd3Nci65ZEymnA7Enfqy_gBoSXK0qdsEDZxxE > 3jJLnplDmm6KovQZHdGX_6u03PKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2F > mailman%2Flistinfo%2Ffreesurfer -- next part -- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1JvBfmBi57GPnae3pffFHMt7spN6t92V5q1T0KcXFfz112mLbY18bi4zNYqaR1fDllzuPRzvHPPZdhJsFy_-JS_5TYCypyTd1DV0gQJ81Vnbun-w1jgpS-nfAm_-xzKpU5Ahvz3D6YuiiBxYVQnnu9El0ohZ5YagIdqXdrc43RZCrThc2UylfmrcEP886ol_DPKenpIizoowtawtzz6jO51KKU2At0huy5rSrNZVc1NMkBOVtnBiLJO4aMh4DTDzbg8Wyv80_vcz45LmZe01n8g/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210216%2Fd3f31b14%2Fattachment-0001.html -- Message: 3 Date: Wed, 17 Feb 2021 17:36:49 +0900 From: ? Subject: [Freesurfer] VB password To: freesurfer@nmr.mgh.harvard.edu Message-ID: <3888b0f5-515a-4637-83f6-38e635234...@fmu.ac.jp> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am attempting to run the Freesurfer Ubuntu virtual box but I need the ?Developed? password. Is it possible to have it? Best Mudathir -- Message: 4 Date: Wed, 17 Feb 2021 08:54:00 + From: "Gronow, Franziska" Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: "'freesurfer@n
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
PS sorry for misspelling your name! It got autocorrected into Francisca and I only noticed one of the wrong c:s Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Iglesias Gonzalez, Juan E." Reply-To: Freesurfer support list Date: Wednesday, February 17, 2021 at 08:54 To: Freesurfer support list Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? Dear Franciska, It’s hard to tell from a single plane, but it seems that dark voxels from the ventricles are mixing with bright voxels from the corpus callosum, into gray voxels looking like the pulvinar and medical nuclei. Would you be able to share the whole subject so I can take a closer look? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Gronow, Franziska" Reply-To: Freesurfer support list Date: Wednesday, February 17, 2021 at 03:54 To: "'freesurfer@nmr.mgh.harvard.edu'" Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? External Email - Use Caution Dear Freesurfer experts, I’ve been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the „Segmentation of thalamic nuclei“ tool by Iglesias, J.E. et al. The „recon-all“ as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases – regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://www.dropbox.com/sh/53fhanytrt4es6e/AAAqEmgl7N5YqpxDYMfxHQDAa?dl=0 Thanks for your help! Best, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
Dear Franciska, It’s hard to tell from a single plane, but it seems that dark voxels from the ventricles are mixing with bright voxels from the corpus callosum, into gray voxels looking like the pulvinar and medical nuclei. Would you be able to share the whole subject so I can take a closer look? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Gronow, Franziska" Reply-To: Freesurfer support list Date: Wednesday, February 17, 2021 at 03:54 To: "'freesurfer@nmr.mgh.harvard.edu'" Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? External Email - Use Caution Dear Freesurfer experts, I’ve been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the „Segmentation of thalamic nuclei“ tool by Iglesias, J.E. et al. The „recon-all“ as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases – regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://www.dropbox.com/sh/53fhanytrt4es6e/AAAqEmgl7N5YqpxDYMfxHQDAa?dl=0 Thanks for your help! Best, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
External Email - Use Caution Dear Freesurfer experts, I've been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the "Segmentation of thalamic nuclei" tool by Iglesias, J.E. et al. The "recon-all" as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases - regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://secure-web.cisco.com/13NyoIuwpnsiHWemQxkjh3X8nFYXTG9wpVXrDAWJsCjxurFVaijSCi6HJ1omS-JnHaipqYf5OTTQWIpbyRGx1_9uZDcFhQbX6Iz_gAK-PbGYNDeH6sLSwTH44gEtwTIIDN3jA24q3bDrmmkiYMtKoLeNzHyjPGySb1cHLbldpyoJgJe3zdizx9tlVc9dPMmRMk-DDBSBpmAmCPpY0ZiHiy612_W6DLESWA4wfED2Qh1qBp1OOpbisCCSiSBzrCY031mQMzsBKD7lNrvAIk8bVHA/https%3A%2F%2Fwww.dropbox.com%2Fsh%2F53fhanytrt4es6e%2FAAAqEmgl7N5YqpxDYMfxHQDAa%3Fdl%3D0 Thanks for your help! Best, Franziska ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
