Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Re: [Freesurfer] Password
by fsbuild 18 May '22

18 May '22

External Email - Use Caution Sending the info ro your email shortly. - R. On May 18, 2022, at 06:08, Pål Gunnar Larsson <pall(a)ous-hf.no> wrote:        External Email - Use Caution        Hello Has downloaded FS_7_2_0_Ubuntu_18_04_06.ova.7z Can you please send me a password? Best Pål G. Larsson M.D., PhD.Senior Medical OfficerDepartment of NeurosurgeryDivision of Surgery and Clinical Neuroscience Oslo University HospitalPo.box 4950 Nydalen0424 OsloNorwayTel:  (+47) 23074407Mobile: (+47) 93429791E-mail: pall@ous-hf.no Ikke sensitiv _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer Passcode
by fsbuild 18 May '22

18 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 16, 2022, at 17:43, Utsav Shrestha (shrstha3) <shrstha3(a)memphis.edu> wrote:        External Email - Use Caution        Hello all,I would like to request for a passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z as being instructed in the wiki. Thank you for your time!With Regards,Utsav ShresthaBiomedical EngineeringClass of 2024Research AssistantThe University of MemphisMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1FX5E_3Dju9d12sGP3CXRycSkIsmTlfB2FGP7… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Password
by Pål Gunnar Larsson 18 May '22

18 May '22

External Email - Use Caution Hello Has downloaded FS_7_2_0_Ubuntu_18_04_06.ova.7z Can you please send me a password? Best Pål G. Larsson M.D., PhD. Senior Medical Officer Department of Neurosurgery Division of Surgery and Clinical Neuroscience Oslo University Hospital Po.box 4950 Nydalen 0424 Oslo Norway Tel: (+47) 23074407 Mobile: (+47) 93429791 E-mail: pall(a)ous-hf.no<mailto:pall@ous-hf.no> Ikke sensitiv

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Problems with identifying fornix using TRACULA
by Morgan Botdorf 17 May '22

17 May '22

External Email - Use Caution Hi all, We recently processed our DWI data (school-aged children) using the updated version of TRACULA (Freesurfer 7.2). We were mainly interested in using this version because of the addition of the fornix to the atlas. After processing the data, we noticed a lot of really small volumes for fornix and noticed that TRACULA had a hard time overall in defining this tract in our dataset. We know that this is a hard tract to define, and we were wondering if there are any suggestions for improving the identification of this tract using TRACULA? <mbotdorf(a)terpmail.umd.edu> Thank you, Morgan Botdorf -- Morgan Botdorf, Ph.D. Postdoctoral Researcher The Changing Brain Lab University of Pennsylvania mbotdorf(a)sas.upenn.edu <mbotdorf(a)terpmail.umd.edu>

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Opening for PhD position based in Tours (Loire Valley, France)
by briend 17 May '22

17 May '22

External Email - Use Caution Dear colleagues, Apologies for double posting, The INSERM-U1253 & University of Tours research unit based in Tours (Loire Valley, France) invites applications for a PhD position to begin in the Fall of 2022 on the reward and interoceptive systems in autism. The main objective of the current PhD proposal is to identify impaired social processing in autism and AD across the last two dimensions. To do that, first, this project will explore the neural activity of the reward system in these patients via functional magnetic resonance imaging. Then, we will probe the deficit of interoception present in these disorders. This sensory modality will also be examined in relation to social processes, within an innovative device of immersive reality (the CAVE: computer automatic virtual environments). Applicants should hold a Master's degree (or equivalent) in one of the following disciplines: computational or cognitive neuroscience, computer science, cognitive science or related. Prior experience in the field of computational neuroscience and/or neuroimaging are of advantage. Sound knowledge of statistics and programming are essential. The candidate’s main missions will be to program, run and analyze behavioral and neuroimaging tests with individual with autism and healthy controls, involving interoceptive tasks and cognitive tests. A good command of written and spoken English is requested of all applicants. Knowledge of French language is beneficial. Prospective candidates should also contact directly Frederic Briend (frederic.briend(a)univ-tours.fr) and/or Marianne Latinus (marianne.latinus(a)univ-tours.fr) by June 2, 2022. Please include the following documents in your application (as a single PDF-file): Cover letter, curriculum vitae, at least one recommendation letter. The position should start in October 2022. For more information, and to apply (deadline: June 2, 2021): Follow this link*, and the how to section here**. Frederic Briend * https://secure-web.cisco.com/1_4aOFbrupfS8UnwlBMZogdhCEcKWAuwy5IJXTH8J0v0Sl… ** https://secure-web.cisco.com/1PI-W3CqSafquqExDKKVrmQEWfUneXHmYuwkE3xSpUzo-W…

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Integrating glmsingle with freesurfer and mri_glmfit
by Lauri Tuominen 16 May '22

16 May '22

External Email - Use Caution Dear FreeSurfer experts, I would like to use mri_glmfit to do 2nd level random effects analysis on fMRI data I fit with GLMsingle: https://secure-web.cisco.com/114IBmtjAcpPLMEdKHUFIkzufzyCZI6VANnXTx7RjQGYq5… >From GLMsingle I get standardized mean difference (SMD) for any given contrast, i.e. beta- difference map weighted by inverted square root of pooled variance. I am wondering if can I just feed those SMD maps to mri_glmfit via mri_concat or am I missing something elementary? Thank you again! Lauri Tuominen

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Perform aseg in Freeview
by R.J. Austerman 16 May '22

16 May '22

External Email - Use Caution Hello, brand new to this software and community so I apologize if this is a dumb question or if I’m asking it through the wrong channels. I understand that Freeview is just a visualizer for Freesurfer, but since I just want to use it to automatically segment brain MRIs for 3D modeling, I wondered if there was a way to do that within Freeview instead of working with it via the command line. Thank you!

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Freesurfer Passcode
by Utsav Shrestha (shrstha3) 16 May '22

16 May '22

External Email - Use Caution Hello all, I would like to request for a passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1Z_58ZIo4a_bMWTqfcqkaCMACuAsrRdQh6f5WruyNMb1Bx…> as being instructed in the wiki. Thank you for your time! With Regards, [UofM logo] Utsav Shrestha Biomedical Engineering Class of 2024 Research Assistant The University of Memphis https://secure-web.cisco.com/1R7Pv-5gfP8NMbNFTlLNdukObQbEhW9E7Rd8vOYudaxHuV…

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Re: [Freesurfer] Permission denied error from -localGI
by Billah, Tashrif 16 May '22

16 May '22

Just closing this thread: we have solved it in https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62 Thanks, Tashrif

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Infant FreeSurfer: volumes extraction without surface
by k3ops＠free.fr 16 May '22

16 May '22

External Email - Use Caution Hi FreeSurfer team, I've been using Infant FreeSurfer for several very young subjects and it works pretty well. But after reviewing the generated surfaces, it looks like pial surface is not extended to fit the cortical grey matter as you can see here: https://secure-web.cisco.com/1bVpNYbCiS9rSsh1DZzM2NKnotXc5MALdQxso7AZkTASVm… (By the way, did you already observed such surface error for infants using Infant FreeSurfer?) I was using this command line to generate the volumes of the brain structures: mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId So now, I would like to generate the volumes of the brain structres whithout any surface information, to avoid any missleading estimates, is this command line appropriate then? mri_segstats --seg mri/aseg_CCseg.mgz --sum stats/aseg-nosurf.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --euler --ctab $FREESURFER_HOME/InfantASegStatsLUT.txt --subject $subjectId >From what I see, most of the structures volume are identical, except that cerebral grey and white is now provided by the labels and not the surface, and supratentorial/totalgray regions are now missing because only provided by surfaces. Is there another way to generate statistical values only based on labels? Do you recommend a more classic approach like counting voxels from each structure of interest and then multiplying by pixel resolution? (which is very tedious and error prone in my opinion) Thanks a lot for your feedback. Florent

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Freesurfer May 2022