Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Postdoc Position
by Didenur Sahin 03 Nov '21

03 Nov '21

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the advertisement below. Best, Didenur Sahin *ANNOUNCEMENT OF POSTDOCTORAL FELLOWSHIP IN FMRI ANALYSIS * Brain Development And Psychosis Lab, National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Centre (ASBAM) & Department of Psychology, Bilkent University, Turkey. The Brain Development And Psychosis Lab is pleased to announce a postdoctoral fellowship position in fMRI analysis. Located within the National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Centre (ASBAM), the Brain Development And Psychosis Lab conducts research in adolescent brain development. The lab's primary mission is to understand the cognitive, neurobiological, and genetic mechanisms that influence an individual's susceptibility to develop serious mental illness (e.g. psychosis, schizophrenia). We seek a candidate with experience in f-MRI analysis. A Ph.D. in cognitive science, engineering, neuroscience, or related field is required. Experience in computational methods used in neuroimaging (e.g., Matlab, Python, SPM) and computer programing is also required. Advanced skill in statistical modeling, and the ability to carry out independent statistical analyses using standard software packages (e.g., SPSS, SAS, R) are desirable. The candidate will have the opportunity to analyze and interpret f-MRI data from an ongoing project on brain development, which aims to provide neurobiological insights into the genetic and environmental mechanisms of risk around the time of life when psychotic symptoms typically appear. The project is funded by The Scientific And Technological Research Council Of Turkey (TUBITAK). Postdoctoral fellows will receive mentoring in clinical/human research methodology and work in a collaborative, multi-disciplinary environment to gain experience in psychosis-centered research. The postdoctoral fellowship position is for 18 months, renewable subject to securing further funding. Please email a CV and cover letter to Prof. Dr. Timothea Toulopoulou (ttoulopoulou(a)bilkent.edu.tr) -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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Total volumes SAMSEG
by Nederpelt, D.R. van (David) 02 Nov '21

02 Nov '21

External Email - Use Caution Dear SAMSEG developers, Is there an easy way/specific function to compute the total volumes (GM, WM and Total Brain) after the cross sectional processing pipeline has been run? I currently add the volumes specified here: MorphometryStats - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1TiZSqlkmJdSG6YomLyN1O5wCUsd9cdQzzIoKCQYS9Wpvi…> However, adding the WM volumes (lhCerebralWhiteMatter + rhCerebralWhiteMatter + WM hypointensities) results in lower volumesthan the volumes found with FreeSurfer. Thank you very much in advance! Best regards, David [cid:image002.png@01D40E30.3E299A80] David van Nederpelt, MSc. | PhD Candidate Radiology and Nuclear Medicine Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands T: +31 20 444 6480 | E: d.vannederpelt(a)amsterdamumc.nl<mailto:d.vannederpelt@amsterdamumc.nl> http://secure-web.cisco.com/1EOtsCiWTwBLCVMkC2cEggLJndUZQC9bJDTTa84lDglqlKV…<http://secure-web.cisco.com/1adKHUXOwhS5An078rgDU8DhS5pGcVaF-bemoEwstJMOWdV…> | http://secure-web.cisco.com/1MykofUmqPylr7OSHojIjyyuz3FqKchVPIVM4VJj6JPJzvT…<http://secure-web.cisco.com/1gpC425-YWhlfpRlTm0wPHu3H0yqPdczn6ZxyBZtVEFl5eb…> / http://secure-web.cisco.com/1IDr1ToLQ00j-N7JGdkZizZ2EY4BfRaX-Ni0bhB33BkT_pJ…<http://secure-web.cisco.com/1wXJqt2HAZw1ZuD0nu0MtMhTFzaeK7O7CKFnLDqQmLsmS7l…> ______________________________________________________ ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/13cespwJDanP8jSeJT-F5DbVhbpJ9dqA3oMmUiNIdESzfsi… AMC disclaimer : http://secure-web.cisco.com/1-TwAPrU-0Wch-3LbY82fTZ4s74MTy5spCul9ZUUp4f7Au_…

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Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found
by fsbuild 02 Nov '21

02 Nov '21

External Email - Use Caution OK, thanks for the feedback.  I was going to suggest “sudo apt-get update”.  Upgrading can also help, though might not always be needed, but good to hear everything works now after those steps and installing the .deb package. - R. On Nov 2, 2021, at 15:23, Alvarado,Luis R <luis.alvarado(a)louisville.edu> wrote:sudo apt-get install ./freesurfer_7.2.0_amd64.deb

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Re: [Freesurfer] Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found
by fsbuild 02 Nov '21

02 Nov '21

External Email - Use Caution Hello Luis, This looks like an issue reported after people upgraded their Ubuntu systems causing the linker to find the wrong version of that library, e.g., https://secure-web.cisco.com/1CpmNJNH8pzSL1hJLa-ZTGnKU7d3M4tiDWoGYjpeLYrLel… https://secure-web.cisco.com/1clrdFLQBdqfAUq5LKlEmqt_gldQ1QZdh66JUXfxroxEcE… As of the 7.2.0 release, there is a .deb installer package you can use if you have admin/root privileges.  If there is an issue with the wrong version of libraries on your system, running the installer might update them. $ wget https://secure-web.cisco.com/1BtJUISuwmua9sN1tMsVUil68Clx5N6mnuRI… $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb - which should give you /usr/local/freesurfer/7.2.0 You can always uninstall it. - R. On Nov 1, 2021, at 20:54, Alvarado,Luis R <luis.alvarado(a)louisville.edu> wrote:/lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found 

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Re: [Freesurfer] Ubuntu developer password
by fsbuild 02 Nov '21

02 Nov '21

External Email - Use Caution Hello James, Sending the info and upgrade instructions to your email shortly. - R. On Nov 1, 2021, at 23:50, James Allebone <james.allebone(a)gmail.com> wrote:        External Email - Use Caution        I installed the Ubuntu image in virtual box to run free surfer on windows - can I have the developer user password?Cheers,James. -- James Allebone | MPsych, Ph.D. (Clinical Neuropsychology)Melbourne School of Psychological SciencesThe University of MelbourneFlorey Institute of Neuroscience and Mental HealthMelbourne Brain Centre, Austin Campus245 Burgundy Street, Heidelberg VIC 3084 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1oWnrmKQcSbthvGFYkNf6v-KNhmGbgq2BWgtuST… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Inflated surfaces on FS7 looking different
by DIANA ORTEGA CRUZ 02 Nov '21

02 Nov '21

External Email - Use Caution Dear FreeSurfer team, I am experiencing a display problem in the FreeView version of FreeSurfer 7 for inflated surfaces. The inflated surfaces from my fsaverage folder look as in the screenshot attached, missing the gyri and sulci coloring and having a see-through pattern. My FreeView version is 3.0 Build Jul 23 2020. One of my colleagues tested opening inflated surfaces using different versions of FreeView, and these also look see-through using a version from FS7, but not using a version from FS6. Have any of you encountered a similar display for inflated surfaces? Do you know if this could be changed? Any advice would be much appreciated!! Thanks a lot. Best, Diana Ortega Cruz. PhD Student Laboratory for Clinical Neuroscience Centro de Tecnología Biomédica - Universidad Politécnica de Madrid

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Ubuntu developer password
by James Allebone 01 Nov '21

01 Nov '21

External Email - Use Caution I installed the Ubuntu image in virtual box to run free surfer on windows - can I have the developer user password? Cheers, James. -- *James Allebone | **MPsych, Ph.D. (Clinical Neuropsychology)* Melbourne School of Psychological Sciences The University of Melbourne Florey Institute of Neuroscience and Mental Health Melbourne Brain Centre, Austin Campus 245 Burgundy Street, Heidelberg VIC 3084 http://secure-web.cisco.com/11YWp3EzHcxEvSJ0KRfhDuEIALHjzrlNAYy_nj3AfpjZa7m…

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Re: [Freesurfer] Base correction, longitudinal analysis
by Eszter Boros 01 Nov '21

01 Nov '21

External Email - Use Caution Thank you for your answer! I think I should clarify this question a little bit. So this is about correcting the Base. And run recon-all *after *correcting the Base. What command should I use here? if I want to regenerate only the Base after correcting it? Because the common below does not work: (ERROR: must specify subjects for base subject using -base-tp) recon-all -base OAS2_0057 -autorecon-pial But if I use "recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all" that just creates a new Base based on the cross MR1 and MR2. My question is how can I regenerate the corrected Base? What command should I use? Thank you so much! All the best, Eszter Boros Eszter Boros <boros.eszter0226(a)gmail.com> ezt írta (időpont: 2021. aug. 8., V, 19:04): > Dear FreeSurfer Team, > > I am working on a longitudinal pipeline and after correcting the Cross and > generating the Base, I can still see some pial problems sometimes (on the > Base). > > I read on the Freesurfer website that it is possible to correct and > regenerate only the Base, but when I use this command: > > recon-all -base OAS2_0057 -autorecon-pial > > /where OAS2_0057 is the name of the Base/ > > I get the following error message: > > ERROR: must specify subjects for base subject using -base-tp > > > Why is this not working? I am using Freesurefer 7.1.1. > > Thank you so much! > > All the best, > Eszter Boros > >

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Problem with FS 7.1.2 binaries: libcrypt.so.1: version `XCRYPT_2.0' not found
by Alvarado,Luis R 01 Nov '21

01 Nov '21

External Email - Use Caution Hi all, I ran into issues running binaries like mri_aparc2aseg, mri_vol2vol, etc. on 7.1.2 $ mri_vol2vol mri_vol2vol: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not found (required by mri_vol2vol) The issue is resolved when I switch back to 7.1.1. I am running Ubuntu 18.04.5 LTS. any help will be appreciated. Luis R. Alvarado Graduate Student Fellow Department of Anatomical Sciences and Neurobiology University of Louisville Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Registering DTI fiber tracts (from MRtrix3) to FreeSurfer registered surfaces.
by Sherin Sugathan 31 Oct '21

31 Oct '21

External Email - Use Caution Hi!!, I have a two time point brain dataset of a single patient. The data consists of structural and DTI for both timesteps. I run FreeSurfer on each timestep separately for generating brain surfaces. When I display the brain surfaces(from both timesteps) together, they were appearing unregistered. Then I figured out that I need to use*FreeSurfer Longitudinal*to fix the registration problem. If I use FreeSurfer longitudinal, then it will most likely register both time point data to a common template, and my registration problem will be solved. I also want to display fiber tracts generated from MRtrix3 along with the brain surfaces generated by FreeSurfer. The problem is that the DTI data will not be touched by FreeSurfer. I am anticipating that this will become a problem to display fibertracts and brain surface properly. Please see below table that shows the data discrepancy I am expecting: |+----------------------------------+-----------------------------------+ | time t0 | time t1 | +----------------------------------+-----------------------------------+ | T1.nii(registered by FreeSurfer) | T1.nii (registered by FreeSurfer) | | DTI.nii (unregistered DTI image) | DTI.nii (unregistered DTI image) | +----------------------------------+-----------------------------------+ | FreeSurfer only takes in the structural data for brain surface generation and it leaves the DTI image untouched. Later, the fiber tracts generated using MRtrix3 won’t align with the FreeSurfer surfaces. How can fix this problem? Do you think it is possible to fetch some transformation and apply to DTI fiber tracts to fix the issue? Thanks in advance Reshma

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Freesurfer