Freesurfer October 2024

freesurfer@nmr.mgh.harvard.edu

44 participants
51 discussions

mri_WMHsynthseg error: Killed 9
by Johnson, Ian 07 Oct '24

07 Oct '24

External Email - Use Caution Hello SynthSeg Experts, I am having an issue when I run mri_WMHsynthseg. I have run the program many times before without any issues. I recently closed my terminal while updating my Mac and reopened it to run WMHsynthseg. I have seen from previous posts that the "killed" error is because of an issue with RAM, but I have not run into this error in the past. The error occurs while on the "Pushing data through the CNN" step. There is no error message, terminal just prints "killed: 9" Best, Ian J

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Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer
by fsbuild 07 Oct '24

07 Oct '24

External Email - Use Caution  Please let us know the operating system name and revision running on the machine. - R. On Oct 7, 2024, at 16:13, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best,Ian Johnson, B.A.Clinical Research AssociateDivision of Neurocritical Care & Emergency NeurologyYale School of MedicineE: ian.p.johnson@yale.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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error: Bad CPU type in executable WMH FreeSurfer
by Johnson, Ian 07 Oct '24

07 Oct '24

External Email - Use Caution Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best, Ian Johnson, B.A. Clinical Research Associate Division of Neurocritical Care & Emergency Neurology Yale School of Medicine E: ian.p.johnson(a)yale.edu

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tkmedit does not start
by Francesco Lomi 07 Oct '24

07 Oct '24

External Email - Use Caution Dear all, I am writing you because I am trying to launch tkmedit on my Ubuntu computer but the program does not start. I get no errors but simply the terminal goes back to a new input line. I have Freesurfer correctly installed because I normally use freeview and recon-all runs without problems. If you had any suggestions they would be highly appreciated Best, Francesco

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Re: [Freesurfer] Freesurfer stopped working after updating to Ubunto 24.04.1 LTS
by fsbuild 05 Oct '24

05 Oct '24

External Email - Use Caution Hello Raj, Sometimes when OS’s update to a new major revision, the system libraries change such that software installed under the old OS version is not backwards compatible with the new OS version.  I think we may have already mentioned on the list that the current freesurfer builds/releases do not yet support installing or running on Ubuntu 24.  VM applications like Oracle’s VirtuaBox, and those from VMware, etc., support making a snapshot and/or backup copy of the VM’s disk image..  So for example, before upgrading from Ubuntu 22 to Ubuntu 24 you could clone the current VM  (as VirtualBox calls it) so that you have a copy (or a 2nd) VM that is your old Ubuntu 22 system.   You just need to have enough disk space to store snapshots and/or clones/backups of the virtual machine.  Sorry I don’t have a workaround to run 7.4.1 on Ubuntu 24. - R. On Oct 5, 2024, at 06:26, Raj Agarbattiwala <raj27289(a)gmail.com> wrote:        External Email - Use Caution        Dear Developers I installed Freesurfer 7.4.1 when using Ubuntu 22 in an Oracle VM on Windows 10 as a host OS. However, I recently updated to Ubuntu 24.04.1 LTS (I still regret it), and after that, Freesurfer stopped working. It shows "bash: /usr/local/freesurfer/7.4.1/ SetUpFreeSurfer.sh: No such file or directory" as an error message. I tried to re-install Freesurfer, and it showed the following error message: The following packages have unmet dependencies: freesurfer : Depends: libncurses5 but it is not installable Depends: libc6 (< 2.36) but 2.39-0ubuntu8.3 is to be installed E: Unable to correct problems, you have held broken packages. I am a Neurosurgeon in Mumbai. I have beginner-level knowledge of programming. Please help me out. Regards Raj Agarbattiwala Jaslok Hospital and Research Center, Mumbai_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/11xpk6NwlTzyo7_bufXgr7-1Uj_QbwYQSmscCI2OEi7z2i…

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Freesurfer stopped working after updating to Ubunto 24.04.1 LTS
by Raj Agarbattiwala 05 Oct '24

05 Oct '24

External Email - Use Caution Dear Developers I installed Freesurfer 7.4.1 when using Ubuntu 22 in an Oracle VM on Windows 10 as a host OS. However, I recently updated to Ubuntu 24.04.1 LTS (I still regret it), and after that, Freesurfer stopped working. It shows "bash: /usr/local/freesurfer/7.4.1/ SetUpFreeSurfer.sh: No such file or directory" as an error message. I tried to re-install Freesurfer, and it showed the following error message: The following packages have unmet dependencies: freesurfer : Depends: libncurses5 but it is not installable Depends: libc6 (< 2.36) but 2.39-0ubuntu8.3 is to be installed E: Unable to correct problems, you have held broken packages. I am a Neurosurgeon in Mumbai. I have beginner-level knowledge of programming. Please help me out. Regards Raj Agarbattiwala Jaslok Hospital and Research Center, Mumbai

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mri_glmfit error: matrix is rank-deficient by 18
by Shawn Flanagan 04 Oct '24

04 Oct '24

External Email - Use Caution *Hi FreeSurfer Developers,* *I am attempting to compute group analysis as described in the FS tutorial and it appears to run but with the following message at the end for each contrast:* Writing results CON-ACLleft maxvox sig=-2.57471 F=9.30914 at index 155198 0 0 seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 CON-ACLright maxvox sig=2.75772 F=10.1304 at index 31842 0 0 seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 CON-ACLtar maxvox sig=2.22177 F=7.75177 at index 69873 0 0 seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 mri_glmfit done *I have searched the list and no similar errors have been reported. Does anyone have thoughts or insights about this? If it is helpful, I have attached the fsgd file, contrast files, script file, and a representative mri_glmfit log file. * *1) FreeSurfer Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460* *2) Platform: Mac Studio M2* *3) Script: * #!/bin/tcsh set study = $argv[1] foreach hemi (lh rh) foreach smoothness (0 5 10 15 20 25) foreach meas (volume thickness) mri_glmfit \ --y ${hemi}.${meas}.${study}.${smoothness}.mgh \ --fsgd FSGD/${study}.fsgd dods \ --C Contrasts/CON-ACLleft.mtx \ --C Contrasts/CON-ACLright.mtx \ --C Contrasts/CON-ACLtar.mtx \ --surf fsaverage ${hemi} \ --cortex \ --glmdir ${hemi}.${meas}.${study}.${smoothness}.glmdir \ --eres-save end end end *Appreciate your time and advice!* *Best,* *Shawn* -- *Shawn Flanagan, PhD* Associate Professor Director, Human Performance Laboratory Department of Podiatric Medicine and Surgery Dr. William M. Scholl College of Podiatric Medicine Neuroscience Program School of Graduate and Postdoctoral Studies shawn.flanagan(a)rosalindfranklin.edu <shawn.flanagan(a)rosalindfrankln.edu>

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Hybrid combination
by Maja Nikolova 01 Oct '24

01 Oct '24

External Email - Use Caution Hi, I want to do tractography on Olfactory bulb in Parkinson Patients but if I use Desikan and Killiany atlas I can't define well Olfactory bulb but cortical parcelation from Desikan is perfect for Neurodegenerative disorders . For functional disorders AAL2 and define Olfactory Bulb is good. My question is can I combine this two atlases and to have *Combine Parcellations:* - *Cortical parcellations* from Desikan-Killiany via FreeSurfer. - *Subcortical and white matter parcellations* from the AAL2 atlas Meaby sound crazy but I think of this and I like to ask does this is possible any way? Thanks in advance, Best Maja

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PetSurfer, PVC uptake of ROI relative to Pons
by zeno Zeng 01 Oct '24

01 Oct '24

External Email - Use Caution Hi Freesurfer experts, Instead of adjusting the 'PVC uptake of ROI relative to the Pons,' I want to adjust it to the 'whole cerebellum.' Are there any parameters I should modify in the command for this? Also, which parcellation or segmentation method would you recommend for this adjustment? Thank you!

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PhD position available/sensory thalamus/developmental dyslexia
by Katharina von Kriegstein 01 Oct '24

01 Oct '24

External Email - Use Caution We are seeking an enthusiastic PhD student with a particular interest in understanding sensory mechanisms of human communication. Task: The task of the successful candidate involves using high-resolution neuroimaging to test for predictive coding mechanisms in the human sensory pathway in typically developed populations as well as in populations with developmental dyslexia. The project is based on prior work of our group listed here<https://secure-web.cisco.com/1eYkFNwS9FN7zHVolDH0xnf7Dq2PeToz4b3PaGM5L5bup8…>. The setting: TU Dresden is one of eleven German Universities of Excellence. The successful candidate will be based at the Chair of Cognitive and Clinical Neuroscience<https://secure-web.cisco.com/1qGAH2dJu90pNwxoYbS7Y6juvJSqgDQ-kidjwgQ3pm48NC…>. The Chair is part of ReDyslexia,<https://secure-web.cisco.com/1PA3bsEfLY6OZN-kdgPonD-JPj0_q_3Pmuu0ibq3J-gqgi…> which is a research consortium of neuroscientists and clinicians that have the aim (1) to better understand sensory pathway dysfunction in developmental dyslexia, and (2) to directly use this knowledge for improving treatment strategies. ReDyslexia includes studies in humans with developmental dyslexia as well as experiments in animal models. Experiments will be performed at the TUD Neuroimaging Centre (NIC<http://secure-web.cisco.com/1B9euS7RTbWQs6UhieoP1iAfAPZQtKflzEo6zYBPMzf0SuZ…>). The NIC is equipped with a research-only MRI machine (Siemens 3T Prisma), MRI-compatible EEG, eye-tracking and noise-cancellation headphones, and a neurostimulation unit including TMS, tDCS, and tFUS. The experimental facilities are supported by experienced physics and IT staff. The TU Dresden Graduate Academy <https://secure-web.cisco.com/1ThIXhNwzW-Vhe99NSgvkuSueEU_Q9xZUZjW1I_bxTtLme…> offers a comprehensive training programme and individual career advice for early career researchers. The Dresden-concept Welcome Centre<https://secure-web.cisco.com/1lIFaP6lw1NR_zF5f6l4e99SbQKbaTDH3MUX7n-gS6mFrx…> facilitates the start in Dresden for international researchers. The position: The PhD position is fully funded (E13 TV-L 75%) and available at the next possible date. More information: The official job advertisement can be found here PDF<https://secure-web.cisco.com/1jNiBTkw1M6UJAE-Ib7raXVeRlcY1PsBKW7TaNOY0czV14…>. If you have questions or for informal enquiries on the post please contact Katharina von Kriegstein (katharina.von_kriegstein(a)tu-dresden.de<mailto:katharina.von_kriegstein@tu-dresden.de>) _ _ Katharina von Kriegstein Professor of Cognitive and Clinical Neuroscience Vice-Dean Faculty of Psychology TUD Dresden University of Technology Chemnitzer Str. 48b, 01187 Dresden Phone +49 (0) 351-463-43145 https://secure-web.cisco.com/1CzroRXZF2PJEcrPWVAU4xGHcirslcxHmAHQJuWAMqWJDv… https://secure-web.cisco.com/1laJ-TJJIUcBtWBNrNJIWkJF0ayhUIJHmzIkWw3ciMwg2a…

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Freesurfer October 2024