Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Tissue fraction effects correction
by Marina Fernández 24 May '22

24 May '22

External Email - Use Caution Dear FS experts, We are planning to correct for tissue fraction effects on T1w/T2w ratio images using PETsurfer, setting the point spread function estimate to zero. My questions are: 1. Does it make sense to correct for tissue fraction effects on T1w/T2w ratio images even when T1w and T2w images were acquired using the same matrix size with identical voxel resolution (i.e., 1mm3)? 2. If that makes sense, which PVC method would work best for correcting tissue fraction effects (i.e., SGTM, MG, RBV) on structural MRI scans? Many thanks in advance. Best, Marina

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Ubuntu + Freesurfer VM passcode
by Sarah Dziura 24 May '22

24 May '22

External Email - Use Caution Hi, Could I please get the passcode for unzipping the virtual image FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1c1JpTzbKs-wKmYazIR87wrbHFTExyh_O3AcXav_KWBe74…> ? Thank you, Sarah -- Sarah L. Dziura, Ph.D. Postdoctoral Research Associate Developmental Social Cognitive Neuroscience Lab University of Maryland, College Park Pronouns: she/her

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pass code to open ubuntu image for windows
by Juan Ruiz de Miras 23 May '22

23 May '22

External Email - Use Caution Hi, Following the instructions on your web page, with this email I ask you for the pass code to open the freesurfer ubuntu image for windows. Regards, Juan.

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New Postdoc Position in Neuroimaging and Machine Learning in Aging and Neurodegenerative diseases
by Joana Braga Pereira 23 May '22

23 May '22

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 Associate 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 Postdoctoral fellow will have the opportunity to work in a friendly and dynamic environment, be involved in many projects, collaborate with group members on different studies, learn new skills, interact with researchers with different backgrounds and from other universities, analyze large datasets from well-characterized cohorts, apply for grants and develop a wide network of international collaborations. The ideal candidate should have the following qualities: - A PhD in medicine, neuroimaging, computational science, physics, neuropsychology, statistics or a related field. - Experience in statistical techniques, programming, and scripting in MATLAB, Python, R or other softwares. - Experience with structural MRI, DTI, fMRI and/or PET imaging analyses. - Experience with different softwares such as SPM, FSL, FreeSurfer, AFNI, etc. - Experience or interest in working with aging and/or neurodegenerative disorders, particularly Alzheimer’s and Parkinson’s diseases. - Good academic record with scientific publications in world-class journals 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/1Ed62KOtM1rXHyrKg0uzBi4mJwpIswU1t2v-GHYNsF-kVb… (Deadline: 10.Jun.2022) For further information or general inquires, please contact Joana B. Pereira at jbragapereira(a)gmail.com or joana.pereira(a)ki.se. Best wishes, Joana

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The DPABINet Brain Network Open Course is freely available online now!
by YAN Chao-Gan 23 May '22

23 May '22

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Re: [Freesurfer] Passcode for FreeSurfer VM
by fsbuild 23 May '22

23 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 16, 2022, at 06:07, Aleksandra Petrovskaia <alexvalpetrovskaya(a)gmail.com> wrote:        External Email - Use Caution        Dear all,I hope you are doing well. I am an intern at the University of Gothenburg, Sweden,  could you please provide me with a passcode for FreeSurfer VM image? I would like to use this version: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1K6vBdJsncsO4FArAm6uohxZsPHj-p7u1Ssztq… wishes,AlexandraБез вирусов. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1i9mfmQBWSvZ95AjICCQzNHTSucxu_A-YuQ2d_G… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_surf2surf error
by Zhang, Fan 19 May '22

19 May '22

External Email - Use Caution Hello Everyone, I am trying to run mri_surf2surf. But I got some errors saying "no such file or directory" while in fact there are files in the pathway. I was able to run this previously, so I am not sure if this is relevant to the recent upgrade of the Mac operation system (12.2.1). My FreeSurfer version is (Darwin-OSX-stable-pub-v6.0.0-2beb96c). Does anyone know how to resolve this? Thank you so much for the help! Fan mri_surf2surf --hemi lh --s fsaverage5 --sval lh.CCn_band.Seed1_20220314.V1.13subjs.mgh --fwhm 13 --tval lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh sysname Darwin hostname Hans-iMac-Pro.local machine x86_64 user fanzhang srcsubject = fsaverage5 srcval = lh.CCn_band.Seed1_20220314.V1.13subjs.mgh srctype = trgsubject = fsaverage5 trgval = lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 13 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere.reg Loading source data MRIallocSequence(0, 0, 0, 0): bad parm No such file or directory Segmentation fault: 11

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questions about ThalamicNuclei.sh, segmentHA_T1.sh, segmentBS.sh
by Wenjun Huang 19 May '22

19 May '22

External Email - Use Caution Hi, I'm attempting to use segmentThalamicNuclei.sh( https://secure-web.cisco.com/1RV2omTbdlZNcuz2LjtNOfF_gXU-a1Zh7ZafxTa7vX-y1Z… ),segmentHA_T1.sh( https://secure-web.cisco.com/1LhDcP1FH1KgfwvDWIRfvii3lB4d3_LJAyFBfDkPRA2sC_…) segmentBS.sh ( https://secure-web.cisco.com/1Zcp3K-vS0QBfdAhIw0PbtQM6onkntbEtV2RlFJ3B_lENy…) But I have done all the recon-all on version 6.0. So I wonder if it's ok if I run recon-all on 6.0v and do the three segments on 7.2v within one project? I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Many thanks, Wenjun 1) FreeSurfer version(recon-all): freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55 2) aFreeSurfer version(segmentThalamicNuclei.sh,segmentHA_T1.sh,segmentBS.sh): freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 3) Platform: Ubuntu 18.04 LTS(Bionic Beaver) 4) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

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fspalm: mri_surfcluster error: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
by Wenjun Huang 19 May '22

19 May '22

External Email - Use Caution I'm attempting to use fspalm ( https://secure-web.cisco.com/1zRz_KYc-Z02lCLizE3BUB2We3AfuiVlIxzRg5VijNOs5j…) and I copied fspalm, mri_volcluster, and mri_surfcluster into $FREESURFER_HOME/bin. But get error: MRISread(): could not open file mri_surfcluster: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white---------------------------------------------------- Reading source surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white And after I copy mri_volcluster, and mri_surfcluster into $FREESURFER_HOME/bin, I got this error when I run mri_glmfit-sim. I wonder if it's because of my freesurfer's version? And if it works for me if I get a newer version, will it be ok if I recon-all, mri_glm-stim, mri_glmfit-sim on 6.0v and do the fspalm on 7.2v within one project? I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the fspalm.log and in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a 2) Platform: Ubuntu 18.04 LTS(Bionic Beaver) 3) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) fspalm.log and perm.th40.abs.mri_glmfit-sim.log: see attached

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Password Request Ubuntu
by Soto, Valentine C 18 May '22

18 May '22

External Email - Use Caution Hello, I am trying to download the virtual image for Ubuntu to utilize the windows VirtualBox FreeSurfer software. There's a password protecting the download, and I believe this is the email to request access from. Can I get the password for the file? Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1R0ie-9Mo-_ypVxMaHm07Tjd_A2gwb7FA-6sned-VCSHW4…> Sincerely, Valentine Soto, B.S. (he/him) Lulu Merle Johnson Fellow, University of Iowa Interdisciplinary Graduate Program in Neuroscience Neurodevelopment and Psychopathology Lab

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Freesurfer May 2022