Freesurfer November 2021

freesurfer@nmr.mgh.harvard.edu

77 participants
118 discussions

Help
by Nilab Nasrullah 18 Nov '21

18 Nov '21

External Email - Use Caution Hi, I am editing about 120 subjects for a research project. In some reconstructions, the grey matter boundary is not recognised, thus Freesurfer classifies it as white matter. I have tried to remove additional pial surface in the area and it gets a bit better. I have also tried to erase the wm that is classified as gm but the results don't change. Using control points is useless since the white matter is classified correct. Is there any way I can edit the subject to get better boundaries for the grey matter? Thank you for your help in advance. //Nilab Nasrullah När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/15j2MT98v_oiKQhHBGfuJhMcwjnzZPBW7DMojlJbPAlvTd…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1DlyxTNQzYpSS-fXeLORGmWPkKUEgUdunIz5JVvQmQ8_9o…>.

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Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)
by fsbuild 17 Nov '21

17 Nov '21

External Email - Use Caution Hello, Xuxiao, You need to go to this URL, https://secure-web.cisco.com/1crNBAUgLZ3m6E0Fhbayk9W3IGxcTGzIN3PT…, fill out the form and agree to the terms of the freesurfer license.  Then you will be able to download a license file. - R. On Nov 17, 2021, at 06:10, 许霄 <xuxiao(a)xii.ac.cn> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, According to your reply, I found that xeyes worked, but there was no license file. I thought the license file would be created automatically after installation of freesurfer, or by the command "echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc". Do I need to create a license file manually?-----原始邮件-----发件人:fsbuild <fsbuild@contbay.com>发送时间:2021-11-17 10:16:00 (星期三)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xuxiao@xii.ac.cn主题: Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)        External Email - Use Caution        Hello Xuxiao, In a terminal window in Ubuntu running under WSL, please try just running a simple X windows program like xeyes to test that your X-server is running on Windows, $ xeyes(see attachment for what it should look like)Keep an eye out for a flashing X server icon at the bottom of your Windows desktop.  You may have to click on that flashing icon for the xeyes X window to open.  But if you can’t display something simple like xeyes with the X server on Windows 10, then freeview is not going to work.If you installed the Xming X-server on Windows, then you should see an X icon on your desktop that you can click on to start the X-server.  And you can check you see the X icon in the “hidden” area at the bottom of the screen which shows the X server is running on Windows.  See the bottom of this page for how to see Xming is running and then scroll up to see the X windows desktop icon, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1H_CTeKTz6NdVgYALgwJR96KSB3QipiR_myHy5… xeyes works, then check your freesurfer license file can be found.  One way to do that is to set the environment variable FS_LICENSE to the absolute path to your license file.  So you could for example call your license file “license.txt” and copy it into your home directory (denoted by the environment variable $HOME).  You can also set FS_LICENSE in your shell init file.$ cd $HOME$ pwd<output deleted>$ ls license.txtlicense.txt$ export FS_LICENSE=$HOME/license.txt… check it can be read …$ cat $FS_LICENSE<output deleted>Now set FREESURFER_HOME, source the setup environment script as you did in the screenshot you sent below, and try running freeview with no arguments to see if a blank window opens.$ freeviewAnother thing to consider is to try and install the latest version of freesurfer (7.2.0) using the Ubuntu .deb package installer from https://secure-web.cisco.com/1ZL6MYJBHRf57DH2b32bhIZVsh9Do26VHKbPCwa6qZJKfj… and install it with,$ sudo apt-get install ./freesurfer_7.2.0_amd64.debThen you should see 7.2.0 installed as something like /usr/local/freesurfer/7.2.0 which you would use for FREESURFER_HOME- R.On Nov 16, 2021, at 07:26, 许霄 <xuxiao(a)xii.ac.cn> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I can't access the website of archives, so I have to ask questions in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials  FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu) After adding the license, when I tried to run the 'freeview' command to test if everything works well, an error popped out: Segmentation fault(core dumped). more information about my freesurfer environment is shown as attached. Could anyone help me figure it out? Thanks in advance.<freeview-Segmentation fault.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Fwd: OpenNeuroPET hackathon at MGH -- Dec 6th and 7th
by Douglas N. Greve 17 Nov '21

17 Nov '21

For those interested in PET and BIDS, this should be pretty useful. -------- Forwarded Message -------- Subject: OpenNeuroPET hackathon at MGH -- Dec 6th and 7th Date: Wed, 17 Nov 2021 19:31:48 -0500 From: Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> To: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Hi Doug, I was hoping you could forward this to anyone you think may be interested. Thanks. We are hosting a hackathon on Dec 6th and 7th in close collabration with the OpenNeuroPET group (openneuropet.github.io). The goal of the Hackathon is to educate researchers about the new BIDS-PET standard, to help researchers curate BIDS-PET datasets and to discuss how to build and execute pipelines that can operate on BIDS datasets. We are also super interested in multi-modal imaging more generally. Details can be found here: https://github.com/openneuropet/outreach/tree/main/Brainhack-MGH2021. Please reach out to Paul Wighton (pwighton(a)mgh.harvard.edu) if you have any questions or would like to give a talk or have a project you would like to propose. If you'd like to attend some or all of the talks either virtually, or in person (for MGH employees only due to COVID) but don't have the bandwidth to give a talk or work on a project, that's ok too! -Paul

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Using Mri_vol2surf
by m-maiworm＠web.de 17 Nov '21

17 Nov '21

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hippocampal subfield segmentation with DCM
by Wei Shao 17 Nov '21

17 Nov '21

External Email - Use Caution Hi, FreeSurfer experts I'm wondering if there is a way to do hippocampal subfield segmentation with T2 DCM images, instead of NifTi. like this ADNI_002_S_0295_MR_Axial_T2-Star__br_raw_20110602125226394_36_S110471_I238619.dcm Best, Wei

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[recon-all error] Excessive topologic defect encountered
by Alec Süwolto 17 Nov '21

17 Nov '21

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FREESURFER - Re-con all problems
by Alison McDonnell 17 Nov '21

17 Nov '21

External Email - Use Caution when i run recon all it creates all the subfolders but they're empty. the only thing that is actually generated is orig.mgz and rawavg.mgz in the mri subfolder. i didn't get any errors when running recon all so was hoping someone could shed some light on this. Many thanks

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FSGD and Contrast file for scanner and sex correction
by Thalhammer, Melissa 17 Nov '21

17 Nov '21

External Email - Use Caution Dear Freesurfers, I am struggling with the group analysis (FT vs. PT) to investigate cortical thickness while correcting for scanner (4 sites) and sex. I have posted a question already regarding the handling of discrete variables and I got to know that all discrete variables should be treated as classes rather than variables in the FSGD file. However, I have difficulties implementing the correct Contrast file right now. My classes are the following: PTMaleScanner1 FTMaleScanner1 PTMaleScanner2 FTMaleScanner2 PTMaleScanner3 FTMaleScanner3 PTMaleScanner4 FTMaleScanner4 PTFemaleScanner1 FTFemaleScanner1 PTFemaleScanner2 FTFemaleScanner2 PTFemaleScanner3 FTFemaleScanner3 PTFemaleScanner4 FTFemaleScanner4 where the two groups FT vs. PT should be compared while regressing out scanner and sex. As far as I understood, we need "1 -1" for the group difference as well as "1 -1" for the gender difference. But how should the complete contrast matrix look like? Thank you in advance! Best, Melissa

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Full-time post-doctoral position at Barcelonabeta Brain Research Center
by Juan Domingo Gispert López 17 Nov '21

17 Nov '21

External Email - Use Caution The Barcelonabeta Brain Research Center (BBRC) invites applications for a full-time post-doctoral position within the context of the ALFA Study, as part of the Neuroimaging Research Group from the Alzheimer’s Prevention Program. *Responsibilities* - Lead and/or collaborate with other researchers neuroimaging analyses of the ALFA+ and related studies - Prepare publications, presentations and internal project reports - Contribute to BBRC’s scientific work in the field of imaging - Required qualifications, competences and technical skills The ideal candidate will have a PhD in a related field with extensive knowledge in the analysis and interpretation of results obtained though human brain imaging (MRI, PET) and with a thorough understanding of Alzheimer’s pathophysiological processes, particularly at preclinical stages. Excellent communication and writing skills in English are necessary as well as the ability to think independently and work collaboratively. *Selection Process* - Pre-selection: The pre-selection process will be based on qualifications, expertise and motivation reflected on the candidate cover letter and CV. It will be merit-based. - Interview: Preselected candidates will be interviewed by an internal scientific committee. - Offer Letter: Once the successful candidate is identified the Human Resources department will send a Job Offer, specifying the start day, salary, working conditions, among other important details. *Benefits* We offer a unique research opportunity in a highly innovative project in a multidisciplinary institution. - Starting date: ASAP - The position is scheduled initially for 3 years - Salary will depend on experience and will be in accordance to BBRC’s salary scales. - We offer and promote a diverse and inclusive environment and welcomes applicants regardless of age, disability, gender, nationality, ethnicity, religion, sexual orientation or gender identity. *Application process* To apply, please submit a single PDF file containing the following: - Cover letter addressed to Dr Juan Domingo Gispert describing research interests and relevant background - CV - The names of up to three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: rh(a)barcelonabeta.org Subject: Post-Doctoral position in the Neuroimaging Research Group Deadline: December 30th 2021 Click here <https://secure-web.cisco.com/13cwhRjdcRHPPe-8xDp2j2y8N9AFYRuVUoin8qYoM_J4tj…> for additional info. -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://secure-web.cisco.com/1zP4b-68JcaLTeuY7cv5dEnYFEXTatDJltZ18aK8PV3H4D…> 08005 Barcelona <https://secure-web.cisco.com/1zP4b-68JcaLTeuY7cv5dEnYFEXTatDJltZ18aK8PV3H4D…> http://secure-web.cisco.com/15a2Ixd8m4Qhdy_9LDhNwmw6ChXiqFErJn3z25MWJLZyb4p… http://secure-web.cisco.com/1sBhbeGpbzUZ0csHOvR17uMKvE4MHbWTAGCbmwi0Y49SCvi… ------------------------------ Confidencialitat correu electrònic BBRC <https://secure-web.cisco.com/153Q9mbmJOHl6fAJ-x4o5vN8ZuG3r4-nGX20X54CZjW0D5…>. Confidencialidad correo electrónico BBRC <https://secure-web.cisco.com/1Et8vH3ow2yrmwIfvJzHkVQgyzEsKoEA_NPq8joFXk5FOa…>. E-mail confidentiality BBRC <https://secure-web.cisco.com/1tqmgN9YeJMg9QrjBSUGkT6v3QfftbgXk1-69Uvcz8_Pn4…>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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recon-all
by a Chinese reader 17 Nov '21

17 Nov '21

External Email - Use Caution Dear Freesurfer experts,When I run the command "recon-all -s <> -qcache" , ERROR: cannot find /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.thickness Could you help me solve this problem? Thanks in advance.

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Freesurfer November 2021