Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

Re: [Freesurfer] Cortical thickness on version 6 vs 7
by Xiaojiang Yang 12 Mar '21

12 Mar '21

External Email - Use Caution Thank you Matt for letting me know that. John For what it’s worth, we had problems with FreeSurfer 7.X with surface placement accuracy on HCP-Style data (i.e. 0.8-0.7mm isotropic T1w and T2w) and have continued to recommend using FreeSurfer 6 for the HCP Pipelines for now. We usually quote 2.6mm average cortical thickness for young adults, but it does depend on age. Matt. From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Xiaojiang Yang <xjyan...(a)gmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, March 12, 2021 at 10:29 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Cortical thickness on version 6 vs 7 External Email - Use Caution Dear Freesurfer developers, I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7. When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm. According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm. Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you! John.

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Fwd: Hippocampal subfield segmentation
by Wei Shao 11 Mar '21

11 Mar '21

External Email - Use Caution ---------- Forwarded message --------- From: Wei Shao <wshao(a)research.baycrest.org> Date: Thu, Mar 11, 2021 at 11:38 AM Subject: Re: [Freesurfer] Hippocampal subfield segmentation To: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Hi, Freesurfer experts I have tried different T1 and T2 inputs for recon-all and subfield segmentation. As you can see, the left is the axial_T1 scan for recon-all and reoriented T2 scan for subfield segmentation. The right is the sagittal_T1 for recon-all + original_T2 for subfield segmentation. The automated segmentation looks better after reorientation but It seems like there are more “wrinkle” after the re-orientation I also check the original T2 scan, there are a few "Wrinkles" but overall it is good (no wrinkles in hippocampus areas, I guess). Could you tell me how to erase these “wrinkles”,(if possible)? Best, Wei [image: 11958_L.PNG][image: BAY11958_R.PNG] On Tue, Mar 9, 2021 at 2:36 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > Hi again, > > I think the problem is that the T1 and T2 were in different RAS spaces > (maybe a problem when converting the DICOMS?) > > Can you please try again, but using this version of your T2 scan? It’s the > same voxels, but with a rotation + translation in the header (see attached > screenshots). > > Cheers, > > /E > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > > > > > > > > *From: *Wei Shao <wshao(a)research.baycrest.org> > *Date: *Tuesday, March 9, 2021 at 13:06 > *To: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Done. > > > > On Tue, Mar 9, 2021 at 12:29 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > Thanks, Wei. I’ll need the T2 scan, too, to reproduce the error… > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/1Fx61iJxDyYVe2fnrRp0RtspkT-zKv5Bc7Y63jGXjLR_cqD…> > > > > > > > > > *From: *Wei Shao <wshao(a)research.baycrest.org> > *Date: *Tuesday, March 9, 2021 at 10:50 > *To: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Yes, that's right. > > > > On Tue, Mar 9, 2021 at 8:53 AM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > Thanks, Wei. > > Just to confirm: It is BAY11958.rar, isn’t it? > > Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/1zPyhHavtDe-BOf3ONc0w_hrwPGxdAWLBdw_UFdk6DvDm2I…> > > > > > > > > > *From: *Wei Shao <wshao(a)research.baycrest.org> > *Date: *Tuesday, March 9, 2021 at 01:16 > *To: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Hi, Dr. Iglesias > > > > These are the files I uploaded before. > > > > Thanks for your suggestion, I have uploaded the subject as well. > > > > Best, > > Wei > > > > On Mon, Mar 8, 2021 at 9:26 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > (sorry, I hit “send” by accident) > > > > If these are indeed your files: the hippocampal segmentations seem to be > there for both hemis, am I missing something? > > > > If these are not your files: please upload the whole subject (not only the > mri directory) as a single zip file. > > > > Cheers, > > > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/1dN2TtIR95Q_e7HDyPOAO1rPpEjgUKkGjmDO6ykSOveSEnT…> > > > > > > > > > *From: *Wei Shao <wshao(a)research.baycrest.org> > *Date: *Monday, March 8, 2021 at 20:10 > *To: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Hi, Dr.Iglesias > > > > I have uploaded most of the files from mri but some uploading files are > failed due to the permission(I guess) > > > > put: Access failed: 553 Could not create file. (rawavg.mgz) > > lftp surfer.nmr.mgh.harvard.edu:/transfer/incoming> put > orig_nu_defaced.mgz > put: Access failed: 553 Could not create file. (orig_nu_defaced.mgz) > > > > Also, the whole directory > > > > mirror: Access failed: 550 Failed to change directory. > (/transfer/incoming/BAY11958) > mirror: Access failed: 550 Failed to change directory. > (/transfer/incoming/transfer) > > > > If you need any other files, please let me know. > > > > Best, > > Wei > > > > On Mon, Mar 8, 2021 at 9:38 AM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > Happy to hear it’s only one subject! > > You can use the Research Computing Secure File service if you want. > > Cheers, > > /E > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/1CafarPRKDaufU2h-Ym1LPWx_e9ZvgoO6OTY2wq9_75MBpa…> > > > > > > > > > *From: *Wei Shao <wshao(a)research.baycrest.org> > *Date: *Sunday, March 7, 2021 at 16:35 > *To: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Hi, Dr.Iglesias > > > > Sorry for the late reply. > > > > 1 This is a problem that existed in a single subject > > > > 2 The data is on the Server I'm afraid that I might need to ask > administrators to install FTP module before I can upload it. FileDrop has > removed and I'm not sure I can use Research Computing Secure File service > <https://secure-web.cisco.com/1eBAVZsWWR_HCPD2RJhlVuKHa_7f7u6W3sPkSdbuB3GdKu…> nor > not. Do you have a more convenient method for me to upload the file? Thanks > > > > > > Best, > > Wei > > > > On Tue, Mar 2, 2021 at 12:32 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > Thanks, Wei, they look fine… > > Two more questions: > > 1. Is this a problem with a single subject or a more general thing? > > 2. Would you mind uploading the whole subject directory to our FTP so I > can take a look? > https://secure-web.cisco.com/122B5Ozj3vqhOd7S4iEyZWCdDjb91Ert2uOyO9hFEwx0hv… > <https://secure-web.cisco.com/1l9A6PhiKog1O8l0piwPOJ6bVu4No6QoNXKbm9BKNoWk2K…> > > Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/1qOJOLNYddAE1LFZgcFcqi_Px5RF7gEt4AaZLTL5qeaUwNe…> > > > > > > > > > *From: *Wei Shao <wshao(a)research.baycrest.org> > *Date: *Tuesday, March 2, 2021 at 12:29 > *To: *"Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Hi, Iglesias > > > > It's ok. > > > > Here is the aseg.mgz, I'm not sure whether this is good enough? but I > have attached the norm.mgz and aseg.mgz in case you want to check. > > > > > > > > > > Best, > > Wei > > > > On Tue, Mar 2, 2021 at 11:43 AM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > Sorry for the autocorrect! Wei -> way > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/185AprJjk1YWZOkgwrwFKQd7HgW56kk_VXXxriE36u523IX…> > > > > > > > > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Wei Shao < > wshao(a)research.baycrest.org> > *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Monday, March 1, 2021 at 23:40 > *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Hi, Dr. Iglesias Gonzalez > > > > Here is the full log, Thanks > > > > Best, > > Wei > > > > On Mon, Mar 1, 2021 at 10:33 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > > Dear Wei, > > Can you please provide us with the full log? > > Cheers, > > /E > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1tu5fnMeuCfd4PAGogGjLcVRKUH82CGckdst6XLxnxFSbW2… > <http://secure-web.cisco.com/1QG7uGIHTOdZ2Mb_tpU68iZ_owRYsTQl1DBCO6QrSAb64Kb…> > > > > > > > > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Wei Shao < > wshao(a)research.baycrest.org> > *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Monday, March 1, 2021 at 21:14 > *To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] Hippocampal subfield segmentation > > > > * External Email - Use Caution * > > Hi, Freesurfer expert > > > > I tried Hippocampal subfield segmentation with an additional T2 scan by > using FS7.1.0 > > > > Here is the log error massage > > > > Attempted to access cropping(1); index out of bounds because > numel(cropping)=0. > > Error in applyCropping (line 7) > > > > Error in segmentSubjectT1T2_autoEstimateAlveusML (line 950) > > > > MATLAB:badsubscript > @#@FSTIME 2021:03:01:20:38:39 > run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 e 243.67 S 3.47 U > 220.01 P 91% M 1248336 F 144 R 909119 W 0 c 49601 w 14948 I 320352 O 429920 > L 30.66 34.91 35.10 > @#@FSLOADPOST 2021:03:01:20:42:43 > run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 18 47.20 43.27 38.55 > Linux gra813 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC > 2020 x86_64 GNU/Linux > > T2 hippocampal subfields exited with ERRORS at Mon Mar 1 20:42:43 EST 2021 > > For more details, see the log file > /home/weishao//BAY11958/scripts/hippocampal-subfields-T2.T2.log > > > > Could you tell me how to fix this? Thanks. > > > > > > Best, > > Wei > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1KRElfcByalckdH0eSE8KoyDaKBoB93IA7qkOJJEYYynjO… > <https://secure-web.cisco.com/1yoXS6dKZ-NgQmNn6ZWsu7E6Fy28mmAvwujVOWjd0TXC-2…> > > 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 > http://secure-web.cisco.com/1fbEBF3dojblctBXJdzmGvBItNipo3eitWhFwcRkSgDNJE8… > <http://secure-web.cisco.com/1R68pf7p85zJ02q1oq5kuPbw0ArfxqytVfCI8rwt08C8JH7…> > . 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Matlab version 2012b installation problem
by Georgia Kapizioni 11 Mar '21

11 Mar '21

External Email - Use Caution Dear Freesurfer experts, I am trying to install Matlab version 2012b but a message appears: command not found. Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl https://secure-web.cisco.com/1aj9gsBgtgn7YY-Cjp-4RTDQ9ZZ-zSt6U2uLhCNs0DAt-2… -o fs_install_mcr && chmod +x Then I typed: fs_install_mcr R2012b and I receive: command not found. My FS version is 6 and I have already install Matlab2016_b on my Mac. Could you please help me resolve this issue? Thank you in advance, Georgia

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 11 Mar '21

11 Mar '21

External Email - Use Caution Here are the norm.mgz files of two subjects as .zip file: https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzI… Thanks for your help! Best regards, Franziska

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Postdoctoral Research Assistant on the neuroscience of visual processing and decision making
by Etienne B. Roesch 11 Mar '21

11 Mar '21

** Postdoc opportunity ** for neuroscientists and/or neuro-enthusiast engineers We are seeking to appoint a highly motivated, adventurous, interdisciplinary neuroscientist to help us understand how humans prioritise information in support of the decisions they make. We focus on visual perception, attention and individual differences, and will be using psychometrics assessments and psychophysics measurements as well as concurrent EEG-fMRI recording. Full time, fixed term for up to 24 months, with possibility of extension. This role falls in the remit of CHAI, a new £2.4M research project funded by the UK EPSRC and led by the Internet of Things and Security Centre (ISEC) at the University of Greenwich, in collaboration with University College London (UCL), the University of Bristol and Queen Mary University of London, as well as industrial partners. As a follow up to the €1.5M EU project “Cocoon: Emotion psychology meets Cyber Security” (2016-2020) led by us, which measured and established how users of connected Internet-of-Things devices react to cyber security risks, “CHAI: Cyber Hygiene in AI-enabled domestic life” (2021-2024) examines the particular threats posed by Artificial Intelligence. CHAI addresses the challenge of figuring out how to best help users protect themselves against the security risks they will face in a world supported by AI (see: http://secure-web.cisco.com/1CuL6BnF558JaAbIWP-jb9e7cD4U7zHl1-pWk2LQxyAupLd…) The role advertised relates to the fundamental research on human decision making that will inform the technical and pedagogical developments of our partners in the project. The remit is intentionally flexible to allow emerging opportunities for collaborations and includes funding for networking and training. You will have: - excellent computer and statistical skills, including a programming language (Python) - experience analysing neuroimaging data, including EEG and/or fMRI - the motivation to pursue research at the interface between academia and industry This work will be carried out in the Centre for Integrative Neuroscience & Neurodynamics (CINN), in the School of Psychology and Clinical Language Sciences, at the University of Reading. CINN is a research platform currently gathering over 100 research staff and students. It is host to a research-dedicated 3T PRISMA Siemens MR scanner, MR compatible EEG (Brain Products) and TMS (MagVenture) equipments, eye-tracking and versatile computing clusters (incl. cloud management and GPUs), all of which available to the project. Other research projects in the lab currently include the development of a novel Bayesian framework for the analysis of data in psychology and neuroscience, neuroimaging of visual perception and attention, as well as projects with industrial partners on topics as varied as machine learning and brain-computer interfaces for a wide range of sectors. CINN and the School of Psychology are a tight-knit community, committed to open research and reproducibility, at the forefront of what is done in the UK in many ways. The post holder will have the opportunity to participate in many initiatives, and propose new ones, including training events on reproducibility, and best practices in neuroimaging, data analysis and coding, including Software Carpentry workshops. The University of Reading was the first University in the UK to publicly commit to open research. It is one of the first institutional members of the UK Reproducibility Network, and a member of the data and software Carpentries. The University is signatory to the Leiden Manifesto for Research Metrics (http://secure-web.cisco.com/1aBHEAMNXjJYh_EJEn0MRa5fBIIXw7ol-w2THK9rK4UhZah…) is committed to having a diverse and inclusive workforce, supports the gender equality Athena SWAN Charter and the Race Equality Charter, and is a Diversity Champion for Stonewall, the leading LGBT+ rights organisation in the UK. Applications for job-share, part-time and flexible working arrangements are welcomed and will be considered in line with the project’s needs. Deadline: 19/4 Interviews (online): Early may Informal inquiries to Etienne Roesch, e.b.roesch(a)reading.ac.uk More information at: https://secure-web.cisco.com/10lrX3Oyv3Eow-Pw1McJhwDMbop9XenO2pSKRBPwhp8G8o… Etienne — dr. Etienne B. Roesch | Associate Professor of Cognitive Science | Univ. Reading Deputy Director of Imaging, Centre for Integrative Neuroscience and Neurodynamics (CINN) Programme Director, MSc Cognitive Neuroscience, School of Psychology and Clinical Language Sciences meet: Book yourself in my University Outlook calendar www: etienneroes.ch | osf.io/ede88 | github.com/eroesch | rdg.ac.uk/cinn External Email - Use Caution

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Job Post
by Abdou Thiam 10 Mar '21

10 Mar '21

External Email - Use Caution Hello, I hope all is well with you! I would like to post the attached job post on your site. Thanks, Abdou Abdou Thiam Clinical Research Coordinator Stanford University School of Medicine Department of Anesthesiology, Perioperative and Pain Medicine Division of Pain Medicine Stanford Systems Neuroscience and Pain Lab 1070 Arastradero Road, Suite 200, MC 5596 Palo Alto, CA 94304 Phone: (650) -721-4016 | Fax: (650) -725-9642 [cid:image001.jpg@01D38AB2.52B03DD0]

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Re: [Freesurfer] Freesurfer/6.0.0 license
by fsbuild 10 Mar '21

10 Mar '21

External Email - Use Caution Hello We, This page lists how to install Freesurfer 6 including an example command you can run under “Test Your Installation”,https://secure-web.cisco.com/1uXKYTRtJ7KhSIT5Y6Hfq8w0uybgogtK… You could verify the example command works. The message about glibc being newer than version 2.15 may be from the mris_make_surfaces binary which I see included in the git FastSurfer project tree. You can tell what version of glibc your system is running with the command, $ ldd —version Did you try moving aside your current freesurfer license.txt file and downloading a new one ? - R. On Mar 10, 2021, at 11:18, Wei Shao <wshao(a)research.baycrest.org> wrote:        External Email - Use Caution        Hello, Freesurfer expertsI have used Freesurfer/6.0.0 in order to run FastSurfer MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1uv_m5A81P_awQBoh7PdUD3ZAFlDqMHUr1T3d1… copy the latest license.txt into the Freesurfer/6.0.0 home directory.Here is the problem every time I run  FastSurfer,  The attachment is the full log GNU libc version: 2.17ERROR: Systems running GNU glibc version greater than 2.15  require a newly formatted license file (it's free). Please  download a new one from the following page:  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1WwX4YlDWG6EL7gxi6Tpv0IB2qmcgFkC4lwQmcF… you give me some suggestions? Thanks  Best,We<slurm-45540976.out>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer/6.0.0 license
by Wei Shao 10 Mar '21

10 Mar '21

External Email - Use Caution Hello, Freesurfer experts I have used Freesurfer/6.0.0 in order to run FastSurfer https://secure-web.cisco.com/12C5JQprff2Y8YL4t7AWGn9XhCzBPeQ7qRNQPcetjS7kld…. And copy the latest license.txt into the Freesurfer/6.0.0 home directory. Here is the problem every time I run FastSurfer, The attachment is the full log GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://secure-web.cisco.com/1K8wEaOjxHfI-SY43wEEp8bk2OLIpUlwQ6KolO1v5nULkvt… Could you give me some suggestions? Thanks Best, We

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Absolute volume difference between Freesurfer 6.0 and 7.1
by Lee, Sang Hoon 10 Mar '21

10 Mar '21

External Email - Use Caution I recently installed version 7.1, and I compared absolute volumes with version 6.0, and I realized that there are some significant differences in some brain structures (e.g. Hippocampus and amygdala). In some cases, the differences are more than 7%-14%. I understand that I should not be mixing the version when I process my datasets, but can you let me know what the main reason for the differences is, and how much should I expect? thank you. Sang

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 10 Mar '21

10 Mar '21

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 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1F81BC20-3BA0-4A5B-B507-13EED2BEE374(a)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-QoiZKnXiNuQPJicEtr4gYDxjHq1ZrbybgK3HfB2J… ?On 2/23/21, 11:00, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Gronow, Franziska" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Franziska.Gronow(a)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

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