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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of franziska.gro...@uniklinikum-dresden.de> 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 -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von freesurfer-requ...@nmr.mgh.harvard.edu Gesendet: Mittwoch, 17. Februar 2021 14:56 An: freesurfer@nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 204, Issue 33 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/1ak9QaJ1_1rhd69MSCjVvSgBkkgvkfHMc4AJu1OKXYs9k4pS-cXKoec4wiYPdDwg42lFLhj-haNv_GCV3Snd16puLCeHA5stbmdlVVtWyi0yA8m5ZoPUlysAuaBeKGDKuHTOzx0kRataF20Nbjkb4OwRlP7Qzj_VWuz3_mulTKpUfgmhnKsMhd2C0a6-7JDU27JTE70NvqsdJbZHa8OJpTUnN4Dc91ezjJKunzolpTFv9X-OQ174u6iZ_1Q8Sxk1efKBLe99Oyk2osGRyl25Zsw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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. Re: overlap/intersection of labels? (Trisanna Sprung-Much) 2. Re: FreeSurfer 7 vs FreeSurfer 6 surface differences (Mike Schmidt) 3. VB password (?????????) 4. Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Gronow, Franziska) 5. Queries in qdec (Koustav Chatterjee) 6. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.) 7. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Feb 2021 21:58:34 +0000 From: Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca> Subject: Re: [Freesurfer] overlap/intersection of labels? To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <d5d39feb-2d09-4051-b15c-49e61bfb8...@mail.mcgill.ca> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Cornelius I found something that computes the overlap of labels across the same vertex when doing some research about this, not sure if this is what you mean: https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4rsX6beTdCfGCkpiAyjUuMFA31V5ClU95ErPkQPZP8TKRthymZKTmx9z4NZ-1Q_VMNlPzPJ7PZG4H-wntegGfigUm5R6ocjIe4fS6bL4_82SxATBarpW8b6rv_vC1VPBn1ZM4Hj4ld7D7l3hMWkgB8zNZaHVjFrDQM4so73Mk3cuFXo4uZfnmiBKYK9XTJlzfFP24H6-tsGIkT4ka-7BQxMKOmF6bzTYzRo0tE8HTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_label2annot See specifically: --nhits <nhits_file> This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer<https://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8fE_QRjLZ5IwPbIC4gnKD6g26N7TVbaIwYLg5BdgQSCFY1LmWY1cDfBL-R49zhRDt-6TzW_S84l6Z-4U3QS-SBlj8HR82qBl0HjcfjS2buz3mtuIQomiilbbafLXzRw1wQSaUnmj1OITA84m-fC1C8HrL430p2kCyyotFmJGKKwiiXBgMYlYljQIFiqINhAJFUVeI9kbMvioqTgmQZvjStJ8ARcmqHgrk_981OzG8NQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurfer> 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2). I know there is also a command merge_labels that may help? Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Dr. Cornelius Kronlage" <cornelius.kronl...@med.uni-tuebingen.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] overlap/intersection of labels? External Email - Use Caution Dear freesurfers, is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations? I only managed to find labels_intersect (which appears to be from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnwCugW0W6FhO8wM0TL2oLO5bi9fjIhtPrBDzhbCqKzcbupsD5PFcOSeF5Q0Rs_J3sJoI9lWbxxbrYbzUv7-bxMiuXfAqo77oTh3OfNCeUFmsk9uuSK8z0-kYvPRfV89c3qUMvDGvWaz4sAtwVH3FXBf11T46qVKtA6pTCyt2sx-P4ee8nfAHn8Aoz2sdWCcPJLXcMFrrUBot8VS3a2wmrELeIOWXwLg6zxRoTGxpHCw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html<https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naUegbdbmI9Bk7UNIwOTDDV40505y4xUMucZzUUWAKig63gNPrAZl0JMYNPDR9rlE4fUcOuQETynMWSKJG67sRNzzZQq8VF7AEsupWpjkrPP17ola-zMVT-3GDtM_dSs0-j76spejYlLevtumd4uKC8BNXwnxiW47uZxy5cBV4IPlI1yL8DP4GKO7QCjCWHuSjiE1xMapPwxOxVnVfHUKM/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html> ) which is awfully slow. In case this is of use for anyone else, I att ached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac. >time labels_intersect precentral.label frontal.label out1.label > >/dev/null real 1m41.862s user 0m31.052s sys 0m30.757s >time bash bash_labels_intersect.sh precentral.label frontal.label >out2.label real 0m0.193s user 0m0.118s sys 0m0.015s >diff -w out1.label out2.label > Thank you and best wishes Cornelius -- Cornelius Kronlage Assistenzarzt Klinik f?r Neurologie | Neurologie mit Schwerpunkt Epileptologie Universit?tsklinikum T?bingen Hoppe-Seyler-Str. 3 | 72076 T?bingen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1KjgBCNQYaDrTlT1adeip-pMCRusOK30t4z1G_yQgRyZo3kOa2YuXaqj29oV3ylwft6iEUAFqZTRKIjSWa7QDhKKl7GVqXD5deei739ikcG1cz-ZnYnTk4qRVMBigcjjI5L7bV8nxuuUwrI8xM9ouH5Y_DBcFow6ktAfjnw-ohVi5FmIWUQtmCdPzES5yvWDpDUm0hZa8YbnS7OcNMsJI3ySFmX48qS1Q32Cyj025MyayeoKoFo1X3ngpfJrOQQnd88uteaOxcxlUSC8jiHcPIA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210216%2F7d64d19e%2Fattachment-0001.html ------------------------------ Message: 2 Date: Tue, 16 Feb 2021 19:27:05 -0500 From: Mike Schmidt <mikeschm...@schmidtgracen.com> Subject: Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface differences To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CAAtzeZ5o=wxrddzwzkbkfamcjgym+rz-4zc34r1pjdanjsn...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Good questions, Andrew. In FreeView, I loaded the .pial files directly. This should rule out the conversion step (mris_convert or my own script) altogether, I think. In the initial javascript viewers, I tried several debugging steps: - I converted each version of {lh,rh}.pial with the mris_convert from each version of FreeSurfer with no difference. The .pial file from FS6 looked OK; the .pial file from FS7 looked mottled regardless of mris_convert version. - In a more complicated pipeline, I tried loading the STL into blender and having it export a gltf file containing only the vertices, then generate and save normals alongside the vertices into a gltf file. Both versions rendered the same in three.js. FS6 was fine; FS7 was mottled. As I did this with a python script, I never actually saw the surfaces in blender. I can try that and see what they look like there. Perhaps I'll see some additional data that would be useful. The difference seems to be stored in the .pial files, though, so blender may assist in suggesting debugging, but is unlikely to solve the problem in my estimation. Thanks for your thoughts, Mike On Tue, Feb 16, 2021 at 2:06 PM Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Mike, > > > > Are you loading the STL files or the original pial files in freeview here? > > > > If the former, have you narrowed down whether this is an issue with > STL conversion or the actual surfaces? FS surface files only store > vertex and face data, not normals. So, is it possible the normals are > being incorrectly computed during the conversion? You could narrow > down whether it?s a conversion issue by converting the *same* lh.pial > file with both > v6 and v7 mris_convert and comparing those STLs. > > > > Andrew > > > > *From: *freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng < > rwa...@mgh.harvard.edu> > *Date: *Tuesday, February 16, 2021 at 1:32 PM > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] FreeSurfer 7 vs FreeSurfer 6 surface > differences > > FYI, translucent surfaces in freeview do not render properly due to > the limitation of old VTK libs being used. I would not use it for > error checking in this case. > > > > Ruopeng > > > > On Feb 16, 2021, at 11:55 AM, Mike Schmidt > <mikeschm...@schmidtgracen.com> > wrote: > > > > * External Email - Use Caution * > > > > Thank you for your response, Doug. I am including two screenshots from > FreeView side-by-side. These are from the same two lh.pial files > mentioned in the first email. > > <freeview_6-vs-7.png> > > They are very very similar and render correctly in FreeView. But when > I set their transparency from 1.00 to 0.25, similar artifacts appear. > > <freeview_6-vs-7-25a.png> > > It's difficult to say which is "right" from this. There's nothing > behind the pial surface to exploit the transparency. But there's a > distinct difference between the two versions. > > > > Thanks again. Happy to assist in figuring this out in any way I can, > > Mike Schmidt > > > > > > On Mon, Feb 15, 2021 at 12:10 PM Douglas N. Greve > <dgr...@mgh.harvard.edu> > wrote: > > Do these show up in freeview? You can turn on the mesh and vertices > > On 2/14/2021 8:48 PM, Mike Schmidt wrote: > > * External Email - Use Caution * > > Hello FreeSurfer Developers and Experts, > > > > I have written a script that reads the binary representations of the > vertices and faces from FreeSurfer's surf/{l,r}h.pial files and saves > them out unchanged to stl and obj file formats for 3D rendering. I > have used it with FreeSurfer 6 and several MRI images, everything working fine. > Processing the identical input, a single T1-weighted MPRAGE MRI, > FreeSurfer > 7 works great and finishes faster than FreeSurfer 6, but we see > strange aliasing on the 3D objects. The aliasing is identical if I > avoid all of my own code and use mris_convert (from either FreeSurfer > version) to generate an stl file from the lh.pial and rh.pial files. > > > > I've spent a lot of time debugging, messing with different materials > and textures, generating vertex normals at different stages, but I > can't find anything that makes any difference except the FreeSurfer > version. I have seen several items in the release notes (*MailScanner > has detected a possible fraud attempt from "secure-web.cisco.com" > claiming to be* > https://secure-web.cisco.com/1Zw7Fk-uWE9mqJoVox1NyJCZKB_dHhgZGtgHufjvQ > 33XGumbxNyjN2Tvx9QiRVUuxNTudMNvGq2VSHOV89pLe_YXRDMtsoF9e2DkzxFuxiSql_a > bLw9-_YP4jgunh4wppJrHZJzI0yFBpt3Q8Su9w7MTOdT29eNLW2xhf76-RSBs2qFnxdtgN > idnxfPWvvYyuLid846qFKsUocV9trE8ZUGnJ-CFIzd7R26qagaz0pSMJNxYBmdumPaacn7 > bPgwUQAuZz4Eqj6wBzGSSOShdjgA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu% > 2Ffswiki%2FReleaseNotes > <https://secure-web.cisco.com/13CisVO6T8EcCjcUaRuDEzQhXfeQOLsLOv_P5ZIR > SrdjGacCLorCd2blyFVgAjSgRkhQEpQQX8mL7NuYQtzJfic5coZdPhhBX4W8D5avplZT7Z > 0aYKMtCUiXXQz026iRPb2S7qEJBiH5qOtkoZXLmAAvddPvzF1sXjBi1P31zemvLfrFegwp > Ho-XKIJ34Oxuf8LuZW1srLiaHuHcK4rxS-RR1retWjCsrV7PxftLc-SxKHJt_G3Fj_xpjz > 6p6A_zrphgLNq76t_kBR5zaEwGGzg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu > %2Ffswiki%2FReleaseNotes>) that may be related, but I'm not sure how > to go about investigating them. > > > > Left cortex images are included, with links if they don't show up in > the email, of the same brain processed with FS6 and FS7. These are > rendered in Firefox with the three.js library. > > > > FreeSurfer 6.0.0 works well with a smooth surface (*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming > to > be* > https://secure-web.cisco.com/19k2LRSZsPHEJbTQep1IjaKGr1kRjQz6okRV9Utnu > 2sE-zIe6xVZy8BRemHa7WsyM0sVEN5OQQdK9bFavmwFt5O0YtRkiY1Go_wrV9XL5rFa2pn > VUfDasJnJNd444YgNSG-sHhYs058eoqewrlPjfhKySntx8acyFN1X-ZQ4JIOFoOfrkZ-7D > -YBS_sm4h_ko88Qay0cyZk2ZSWfITBiQaHS3aeTYJ9meG5Ka9hgoQNqPycRq1P6z9l3hyx > JMVPxKH_jKpTcQIyQb4QxYUFZ2IQ/https%3A%2F%2Fdragonfruit.mfs.ms%2Frh_pia > l_oblique_from_fs6.png > <https://secure-web.cisco.com/1XvK89a9-pam8vLvddRszbm7noUuI0VdVODMPd_Cm8xNp0P5rR47ivTH33eVFRM18F7lInNFhFKYaWtkQGluSZxAYT2Jcrw3ESz5X3Kx5UAC-9YtMdrzKhx90jsEP-1ru_STzZzBqjgbNsiBdN0OFgW5up3YLDaclEMxbiIhy6EHCAY_8H7g-h06Wc7wQL896W7gW4ZDpUxkDWH6ks3EW_Y2vQs9-hhfUkXblb7u7umpfsgFmJFfyHLw_38O1RpRjDQUfFD1q5DRSgUFvwSDszQ/https%3A%2F%2Fdragonfruit.mfs.ms%2Frh_pial_oblique_from_fs6.png>). > This image is of the correctly rendered surf/lh.pial with 149,968 > vertices and 299,932 faces. > > <rh_pial_oblique_from_fs6.png> > > > > FreeSurfer 7.1.1 results in the same size and shape cortex, but > renders strangely with mottled shading of triangles. (*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming > to be* > https://secure-web.cisco.com/1eYljCLOuS6UNik_oMru30064c6RMzIATcZMoUwV1 > owLAOa-N--MAJEs-nw-BxfHrHTVHjiRzlo6Oo2PFoifhAAUTdAjTK7Rt4UuRT8njb9mTQX > wGUjiMIKv6ukG4W1qGQykiR2tVvoB9EZrucM9Qr10_btw-C6V2G4HPewlBkfJgMp4BafOH > VB9lueULlfnGwcnep4HAEmYoOLFmWguQzZyxiFfhfvU3XeUMAW4g2SDqr_L6i0Abw3vF_q > G1-I6tstrGRQeNvXu4eoFjqgmVVQ/https%3A%2F%2Fdragonfruit.mfs.ms%2Frh_pia > l_oblique_from_fs7.png > <https://secure-web.cisco.com/1GxOeNRNQGbKZlmD1nNK_15MWN_jcLmmy_Y43EXlY-D0-n7YLayhuQXzm02oVANOxwladA-4Q48Zyi1e7e1HwNjWKac2dG5bo7tlqaK8oqLP3jk3SE_RIdU8ohiNRt7IC76oX49QPDYW3tfr9bNcpxl2pNXq1NGL4zBErKygPllk1qGZXlAOqEvTNFIdHde-XjzD17RZ-IXwyDMqGpnYPmgPxAZuaNjQvAa7-Rq_Wf6FOUqywwnl82WD_pdz98xp5YVHKGS--m3T_cxqIRswvfw/https%3A%2F%2Fdragonfruit.mfs.ms%2Frh_pial_oblique_from_fs7.png>). > This image is from the same T1 image as above, but processed with > FS7.1.1, resulting in 147,292 vertices and 294,580 faces. > > <rh_pial_oblique_from_fs7.png> > > > > 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: ????????? <m-bak...@fmu.ac.jp> 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 +0000 From: "Gronow, Franziska" <franziska.gro...@uniklinikum-dresden.de> Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <e0fb0db62995422fa94bf518f0a6b...@uniklinikum-dresden.de> 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 <chatterjeekous...@gmail.com> Subject: [Freesurfer] Queries in qdec To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CADnEN_d_T5yLjJEAVkgtgFuKGJe=cxdcbx1cfz7u58zwto-...@mail.gmail.com> 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. Regards, Koustav -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1yecPPzxS51Jcu7kcXqLrmPt3UXo6jbr_LCuTwj4oEez8WEJvjMKJnwWIhCkWR3n4TfYDy1wRHdpfHvNt-xocv3p01d8mKIZwc9SvTYUsWN4SdUJbbMZkF4Tx-S2bKBgv2EkIOH2NBd6ig3BCaiRxHObV_40aTJqB_fjh2iewFyQnYfnsxRS81E1XpdozKZJQt-CP1KsLOnqLxxeq-9wh6FxjygxU85ObYnWmiS7u6sx9jY3vylQf5d7sGiPPxnun5Z5I2ziXKRsNYORU_F1HWw/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210217%2F66b37c52%2Fattachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 149541 bytes Desc: not available Url : http://secure-web.cisco.com/1vjUkdZlP5ZiYzkw5ljyAjR7NewZGX4831dVdNZQsXD2ehHFdT3hx5Y5QpLUC9lgqLRJ8OYm_kswb5ExpXJUFBEJhNtdC8m4QzTvfjEaPXKtjvdp2fa-DHKr3sjUfg7cVxDH3NTorPTXiZvvrqv2lNTfUQI8Cn6YcrQB-JRe0nIU_ahz9nRprSldkP60A6OUPvar-Sgz3d3c1y8pRRW1fV_V6cWILTKVPudl6T4hZ_ZnwknD_iFqnFOVh9Z4SOKeAKV-pJJ6qNFv_FTzE_ZcR2Q/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210217%2F66b37c52%2Fattachment-0002.png -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 111150 bytes Desc: not available Url : http://secure-web.cisco.com/14B1GmZi94tpU_LUxPOYX_JOs2Ppbwe-I1MGa3A-3mEnF8hTn1aEvvHi6E6rzQeHcufPLd3028Z1fXDySEIVD2GflIn8HeorFlrwWdcQkTBikXUbs1_hWnLAtSLRK7zAC1tPqFUu8644mo6XO4TEypNRgNr89g6Ds58CJjO_AH9k13EALfqoNNGqHDioIoOYgU1hmpMyVoxGdSDk0vBEpa9T3L1tpmv4HtqUjxynq74VFO7aj3biR0995DCkECdJx4yFpdUGqnMRenUNCoAAFgQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210217%2F66b37c52%2Fattachment-0003.png ------------------------------ Message: 6 Date: Wed, 17 Feb 2021 13:53:56 +0000 From: "Iglesias Gonzalez, Juan E." <jiglesiasgonza...@mgh.harvard.edu> Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <8402e729-6d5b-4e6a-b214-de4b4a2e8...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" 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://secure-web.cisco.com/1a2Aos4Kl1w9iiiOULtqTahfTwFN1n_4CYUjZ9lKn9szhImDoYyM9kVfbppL-1optSj3f-3aeGPqF99TEl1rXUnVVB9oqH7jA-w3tpS2ANZyvB7pUxckZCh-Rm2_jhf3_M9uoyLTvZ-QqT9f7JZKW1INlUkKWuaw0WeLf6kv2tZeuJq7_SIMQePoh4X7wJyf8xh_ujmlFvFQaqszCIP-8aFMJVtHsyy2Q5UKJFs8VX7pRTjmrVsQUZOTgyLzf4RkU/http%3A%2F%2Fwww.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Gronow, Franziska" <franziska.gro...@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 17, 2021 at 03:54 To: "'freesurfer@nmr.mgh.harvard.edu'" <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://secure-web.cisco.com/1_qtWbkWI1nH8UoIbXBKOKY4c_SUN_wEd6wtRioyuzq4fCTp0SrvziUGvS72r0rkEkF976y61POLs2vS_NVW80a_isIBe2ZMFKBuv832IhfdHhqeKa-kMflnKBhDWqZPkh_F09_AWEvS-bBPaNADVqrhJUaHuyBHeEQaEzmiG0ZgW40I30LS_uAd6ouVSMbWZA3PZahwPab0o3GODuboBzyC_FP5gqpsy8SK7H2mjTf_sPj0Op1JRCjxeE4d7Qdd9P-mI_xeuicBMKxqLyA0ejQ/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/1BkGmVzdomNckqXbzGIPPOmIuThKnM9WpjOH9SZNdChjh5L7pxeX_avIRS_SQRDo1okiAw3xFXtXlKr0_p-8TNdHk3-y8-fYvpN4sd-wcxBHOXCEAEipqZ8DAFT1QUFd-ItVv9CgHLM84VmbzH1Ch7tcGnylFILBncStqY0d0g9cZEWBV2Cd2e6txKFeslbJp4vIqd_u6DieKd3hCjAQBlYGXAd5coEBopoJIeVpN0urKsgTpTpjTCaVE1kdqr3Vf8AdWG6xHhJX2CqduidL5lw/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210217%2F73d57c9d%2Fattachment-0001.html ------------------------------ Message: 7 Date: Wed, 17 Feb 2021 13:56:19 +0000 From: "Iglesias Gonzalez, Juan E." <jiglesiasgonza...@mgh.harvard.edu> Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ba104bda-3989-4909-ab94-14a62ce29...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" 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://secure-web.cisco.com/1a2Aos4Kl1w9iiiOULtqTahfTwFN1n_4CYUjZ9lKn9szhImDoYyM9kVfbppL-1optSj3f-3aeGPqF99TEl1rXUnVVB9oqH7jA-w3tpS2ANZyvB7pUxckZCh-Rm2_jhf3_M9uoyLTvZ-QqT9f7JZKW1INlUkKWuaw0WeLf6kv2tZeuJq7_SIMQePoh4X7wJyf8xh_ujmlFvFQaqszCIP-8aFMJVtHsyy2Q5UKJFs8VX7pRTjmrVsQUZOTgyLzf4RkU/http%3A%2F%2Fwww.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <jiglesiasgonza...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 17, 2021 at 08:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> 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://secure-web.cisco.com/1a2Aos4Kl1w9iiiOULtqTahfTwFN1n_4CYUjZ9lKn9szhImDoYyM9kVfbppL-1optSj3f-3aeGPqF99TEl1rXUnVVB9oqH7jA-w3tpS2ANZyvB7pUxckZCh-Rm2_jhf3_M9uoyLTvZ-QqT9f7JZKW1INlUkKWuaw0WeLf6kv2tZeuJq7_SIMQePoh4X7wJyf8xh_ujmlFvFQaqszCIP-8aFMJVtHsyy2Q5UKJFs8VX7pRTjmrVsQUZOTgyLzf4RkU/http%3A%2F%2Fwww.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Gronow, Franziska" <franziska.gro...@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 17, 2021 at 03:54 To: "'freesurfer@nmr.mgh.harvard.edu'" <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://secure-web.cisco.com/1_qtWbkWI1nH8UoIbXBKOKY4c_SUN_wEd6wtRioyuzq4fCTp0SrvziUGvS72r0rkEkF976y61POLs2vS_NVW80a_isIBe2ZMFKBuv832IhfdHhqeKa-kMflnKBhDWqZPkh_F09_AWEvS-bBPaNADVqrhJUaHuyBHeEQaEzmiG0ZgW40I30LS_uAd6ouVSMbWZA3PZahwPab0o3GODuboBzyC_FP5gqpsy8SK7H2mjTf_sPj0Op1JRCjxeE4d7Qdd9P-mI_xeuicBMKxqLyA0ejQ/https%3A%2F%2Fwww.dropbox.com%2Fsh%2F53fhanytrt4es6e%2FAAAqEmgl7N5YqpxDYMfxHQDAa%3Fdl%3D0 Thanks for your help! Best, Franziska -------------- next part -------------- An HTML attachment was scrubbed... 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