Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

Postdoctoral Researcher in Neuroimaging at Karolinska Institute, Stockholm, Sweden
by Joana Braga Pereira 12 Apr '22

12 Apr '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 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. - Excellent record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. To apply please go to: https://secure-web.cisco.com/1_02gjVybcT6ODyv8ExuxWUpg_0WuTiWWNMhc561CKQhUu… <https://secure-web.cisco.com/1BWNMr2dp7URFelZIl8NRiChBwHke1TRTjwurTtb4ITDZl…> (Deadline: 29/04/2022) 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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Re: [Freesurfer] Pass code
by fsbuild 12 Apr '22

12 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 12, 2022, at 04:33, Wei <wuhanweizh(a)163.com> wrote:        External Email - Use Caution        Dear professors,I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve.. Would you please send me the pass code for help?wzh _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Pass code
by Wei 12 Apr '22

12 Apr '22

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve. Would you please send me the pass code for help? wzh

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Pass code for FreeSurfer VitrualBox VM Images
by Wei 12 Apr '22

12 Apr '22

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 7z archieve. Would you please send me the pass code? wzh

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Re: [Freesurfer] Request passcode VirtualBox image archive
by fsbuild 11 Apr '22

11 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 10, 2022, at 05:36, Caterina Trainito <caterina.trainito(a)synlab.it> wrote:        External Email - Use Caution        Hello,I would like to request the passcode for the VirtualBox image archive "FS_7_2_0_ubuntu_18_04_06.ova.7z", as described in the wiki page: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/VM_67Thank you!Best regards,Caterina Trainito, MScResearcherIRCCS Synlab SDNVia Gianturco 113 / Via Brin 55, Naples, Italy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[IMPORTANT MESSAGE] Subfields & MCR problems solved
by Iglesias Gonzalez, Juan E. 10 Apr '22

10 Apr '22

Dear all, We have recently fixed two problems in the subfield modules using the Matlab runtime: 1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS. 2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this). Kind regards, Juan Eugenio Iglesias http://www.jeiglesias.com

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Request passcode VirtualBox image archive
by Caterina Trainito 10 Apr '22

10 Apr '22

External Email - Use Caution Hello, I would like to request the passcode for the VirtualBox image archive "FS_7_2_0_ubuntu_18_04_06.ova.7z", as described in the wiki page: https://secure-web.cisco.com/18CS92dSpHzbEbaM7FWv6m5pnsisNkx8qwe4hCCmONAupm… Thank you! Best regards, Caterina Trainito, MSc Researcher IRCCS Synlab SDN Via Gianturco 113 / Via Brin 55, Naples, Italy

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recon-all error
by cooperr1＠student.unimelb.edu.au 09 Apr '22

09 Apr '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I've also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper

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Re: [Freesurfer] mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths
by Megan Schendel 09 Apr '22

09 Apr '22

External Email - Use Caution Hello, I am also trying to use mkheadsurf and getting the same errors described in the January topic by user Yong-Jun Lin. https://secure-web.cisco.com/1gWrCRE26r6WP8WhRpdFnJDHSFKaCpEOt6y_UEivpQG5fG… 1. The first error message is "subjdir: Undefined variable.". I followed the thread and also manually defined subjdir 2. Same problems with mris_smooth -n 10 -b /.. resulting in error: MRISwriteCurvature: could not open lh./... and mris_inflate -n 10 -sulc /... resulting in error: MRISwriteCurvature: could not open /... Lastly, I followed the response from Douglas N. Greve <https://secure-web.cisco.com/1ahbUvtJEJ2YIzAb-v2Vq6dQ8vxhI4tzwwkf_H3Yz4GyLG…> to try the new mkheadsurf. When I tried that, the subjdir error went away, but the output paths errors with the mris_smooth and mris_inflate persisted. The end result output files that I need were created, however, so I can go on with my work. But I thought I'd reply to the list and let you know that I'm also getting these path errors. Thanks for any help, Megan MEG Technician Pronouns: she/her The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106

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Freesurfer stats output meaning
by Rafael Navarro 09 Apr '22

09 Apr '22

External Email - Use Caution Hello Freesurfer developers, I am attempting to build a brain age estimator with FreeSurfer output. However, I am having some problems disentangling Freesurfer stats output. I will be using only the Desikan-Killiany atlas cortical segmentation. I have identified these files as useful: aseg.stats -> subcortical segmentation features lhaparc.stats -> DK cortical segmentation left hemisphere features rhaparc.stats -> DK cortical segmentation right hemisphere features lh.w-g.pct.stats -> DK cortical segmentation left hemisphere grey matter - white matter contrast features rh.w-g.pct.stats -> DK cortical segmentation right hemisphere grey matter - white matter contrast features wmparc.stats -> white matter close to DK cortical segmentation areas features However, I checked these two files too: lh.curv.stats rh.curv.stats But I don't have a clear idea of the meaning of the features in those files. For what I understand the features are the mean and standard deviation of the white matter surface and the pial surface. However, these measurements would be redundant if I include the features from xhaparc.stats, wouldn't they? Thanks for your help! ___________________________________ ----------------------------------- || Rafael Navarro González || Ph.D. Student || ETSI Telecomunicación || Universidad de Valladolid || Campus Miguel Delibes || 47011 Valladolid, Spain || e-mail: rafael.navarro(a)uva.es || Phone: +34 672 394 294 ||_________________________________ -----------------------------------

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Freesurfer April 2022