[Freesurfer] Meylin overlay
External Email - Use Caution Dear freesurfer experts, Is there a way to import the individual surface myelin maps from the human connectome project database to freesurfer and use them as overlays? Or can we create them in freesurfer? Mudathir ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] license file not working
External Email - Use Caution Hi Andrew, it works on the "frontend" of our cluster: NAME="Scientific Linux" VERSION="7.9 (Nitrogen)" ID="scientific" ID_LIKE="rhel centos fedora" VERSION_ID="7.9" PRETTY_NAME="Scientific Linux 7.9 (Nitrogen)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:scientificlinux:scientificlinux:7.9:GA" HOME_URL="http://secure-web.cisco.com/1klnZRW4M4WW9ZVKaWotlbPIVMzmb4T29Qe_78f_eVmTDoUgcEiBiiw5Tlc63lzUMN--Y21kFEP_CCOGZhFevGautv0mNoXcqYUdmw3SsWi-iG94jmMauGXSIQGPNdxEmgsVTYPprF-6etRYZMIoyu4rYCK3FLWA4GhEUQmNBBN-0KsNddnKocuKicc7ztuKAIYGAmtAoJZGTnfDahGeSvq-KCO5jqKx9FB8U2W_v3jXsVuHbrLhAnRo42wMsXIMVFA0tUBOpYs919bxPfACPtQ/http%3A%2F%2Fwww.scientificlinux.org%2F%2F; BUG_REPORT_URL="mailto:scientific-linux-de...@listserv.fnal.gov; REDHAT_BUGZILLA_PRODUCT="Scientific Linux 7" REDHAT_BUGZILLA_PRODUCT_VERSION=7.9 REDHAT_SUPPORT_PRODUCT="Scientific Linux" REDHAT_SUPPORT_PRODUCT_VERSION="7.9" But not any more on the nodes: NAME="CentOS Linux" VERSION="8" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="8" PLATFORM_ID="platform:el8" PRETTY_NAME="CentOS Linux 8" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:8" HOME_URL="https://secure-web.cisco.com/155QFGor0BvTWlPUXIVYeBXT-03HZvvbL_y_LFA__5voZlqIklvV3A9iWM50dUr0CmmbnHh3aOye4TpK7jd3sjvBQO7C8SDg5EnqUHFugRNSwIICKvk5EPRFPrTuTxxXBIbG-dpy3h71VyDY3nLMJrdBQ57Lsb_FualDCAbM1J-w2_EfxHFLPPap6E3qDsFmwmprCUus6fZ9h6Wn5xHrRWK2F0oge7qjB9vnZuKx3JpCBSdVoyfWNwfcXVU5HdwsLB0T96aElwgy2MDb06sul3w/https%3A%2F%2Fcentos.org%2F; BUG_REPORT_URL="https://secure-web.cisco.com/1-z9ny04ggwstoxf8wX8eOhQDvv5yOR_STzc_48_IynJfMZzrYIuUG60St8GdD3yjJCNTGWoYzmJ0DgbM21EDQe_ag0huuDf9MHiQqeQyuXKxI7ggayfubotvDh12nkF1GfeOwxEqKO0RblPhtT7xxRBq7BoAOAZ_gZ7g63-R3m2AeIIt3Dk-ZZGkVt_pZauvPldw2QSqZdtmdu5Js43pZumaajfNbrgXf4ufZ6WfLxZUS7f0vP4cD-eTrXo6jw80aDJDm1R24eDQyGdbicBKjA/https%3A%2F%2Fbugs.centos.org%2F; CENTOS_MANTISBT_PROJECT="CentOS-8" CENTOS_MANTISBT_PROJECT_VERSION="8" Thanks in advance, best, Philipp Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Hoopes, Andrew Gesendet: Montag, 15. März 2021 20:29 An: Freesurfer support list Betreff: Re: [Freesurfer] license file not working Hi Philipp, Can you let us know the OS and version you’re running on? The license format was updated for v6. It should be backwards compatible, but it’s possible it’s not anymore on newer systems. thanks Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Saemann, Philipp Date: Monday, March 15, 2021 at 2:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] license file not working External Email - Use Caution Hi FreeSurfer specalists, for some historical reconstruction I had to download an old FS5.3-Version, on a Linux System, untarred etc. - it seems there was no .license = hidden license file coming with the download, and no license.txt file. I requested one (usual link) and received a license.txt file, and put that into the FS home folder. When using the command mri_convert I get the error message that an invalid License file is used. Questions: (1) Is a .license file (so, a hidden file) needed for itself or in addition? (2) Why does a freshly delivered license.txt file not work? (3) Any other solutions or ideas? Bw, Philipp ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] license file not working
Hi Philipp, Can you let us know the OS and version you’re running on? The license format was updated for v6. It should be backwards compatible, but it’s possible it’s not anymore on newer systems. thanks Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Saemann, Philipp Date: Monday, March 15, 2021 at 2:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] license file not working External Email - Use Caution Hi FreeSurfer specalists, for some historical reconstruction I had to download an old FS5.3-Version, on a Linux System, untarred etc. - it seems there was no .license = hidden license file coming with the download, and no license.txt file. I requested one (usual link) and received a license.txt file, and put that into the FS home folder. When using the command mri_convert I get the error message that an invalid License file is used. Questions: (1) Is a .license file (so, a hidden file) needed for itself or in addition? (2) Why does a freshly delivered license.txt file not work? (3) Any other solutions or ideas? Bw, Philipp ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] license file not working
External Email - Use Caution Hi FreeSurfer specalists, for some historical reconstruction I had to download an old FS5.3-Version, on a Linux System, untarred etc. - it seems there was no .license = hidden license file coming with the download, and no license.txt file. I requested one (usual link) and received a license.txt file, and put that into the FS home folder. When using the command mri_convert I get the error message that an invalid License file is used. Questions: (1) Is a .license file (so, a hidden file) needed for itself or in addition? (2) Why does a freshly delivered license.txt file not work? (3) Any other solutions or ideas? Bw, Philipp ___ 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
[Freesurfer] Postdoctoral Researcher in Neuroimaging at Karolinska Institute, Stockholm, Sweden
External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Assistant Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The fellow is expected to be independent, develop his or her own projects, supervise students and show an interest in approaches based on graph theory. In addition, he/she will have the opportunity to develop new skills, analyze large datasets, apply for grants and develop a wide network of collaborations. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, neuropsychology, physics, statistics or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with structural MRI, DTI, fMRI or PET imaging analyses; - Clinical or research experience with aging and/or neurodegenerative disorders. - Good record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. There are also possibilities for a longer appointment after this 2-year period. To apply please go to: https://secure-web.cisco.com/1YHeKp4uDUxxiD2mZPjaEegL3DgIC_jwTdckTsrl1c73drr9LdtQH7l-SIUreEC1_SBMyEaTTSHqnax2eHs-tTGejzNWwyNCX-5F5qY-kAKNFlpbKE1A7ZlI8hCQeKz9AyZco7T8mvJ-vT9-sFkL-NzqEP2enUshTxh_vxPyc1Hp69rwMqAoubjZSWzTihlXOk79hCPkHUo82owZcR6hP33jqCCdOCP4Y2LtCDrQkHhdT6XTQHv51mc9pvY8NMZtBbbsfbHDAFUZ1w5hwa-i8FA/https%3A%2F%2Fki.varbi.com%2Fen%2Fwhat%3Ajob%2FjobID%3A387573%2Ftype%3Ajob%2Fwhere%3A4%2Fapply%3A1 (Deadline: 31/03/2021) For further information or general inquires, please contact Joana B. Pereira at jbragapere...@gmail.com or joana.pere...@ki.se. Best wishes, Joana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
