Freesurfer

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PhD candidate position - high-resolution imaging of the human claustrum
by Zaretskaya, Natalia (natalia.zaretskaya＠uni-graz.at) 22 May '24

22 May '24

External Email - Use Caution Dear colleagues, I would greatly appreciate if you could forward this job announcement to potentially interested candidates. The Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of Psychology, University of Graz jointly with the fMRI Lab (PI: Christian Windischberger) at MR Center of Excellence, Medical University of Vienna are looking for a doctoral candidate to join us in the project dedicated to high-resolution imaging of the human claustrum, one of the most mysterious and least studied areas of the human brain. You will join the Vienna-based part of the team and will be involved in piloting and conducting experiments using 7 Tesla MRI. You will find further details and the official job advertisement text below. --- Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of Psychology, University of Graz jointly with the fMRI Lab (PI: Christian Windischberger) at MR Center of Excellence, Medical University of Vienna is looking for a Doctoral Candidate within the framework of the FWF funded project "High-resolution imaging of the human claustrum" (Project-Assistant; 30 hours a week; fixed-term employment initially for 1 year with a possibility of extension for up to 4 years in total) Project description The project is dedicated to investigating the claustrum, one of the most mysterious structures of the human brain. It is led by the PI Natalia Zaretskaya in Graz and the co-PI Christian Windischberger in Vienna. You will join the Vienna-based part of the team and will be involved in piloting and conducting experiments using 7 Tesla MRI. Project-related publications: * Adam Coates, Natalia Zaretskaya, High-resolution dataset of manual claustrum segmentation, Data in Brief, Volume 54, 2024, https://secure-web.cisco.com/1zeq_ipnEfhXQWA1cKbf1_H6iUzhhXoee44VMGbemOb2mp… * Adam Coates, David Linhardt, Christian Windischberger, Anja Ischebeck, Natalia Zaretskaya, High-resolution 7T fMRI reveals the visual sensory zone of the human claustrum, bioRxiv 2023.09.18.558213; https://secure-web.cisco.com/1XoozScW5lqeJFO6PKFmaXkaXPux1aUn48UIO7n1abH2yi… Your duties * Participation in planning, preparing and conducting 7T fMRI experiments in Vienna, data analysis * Participation in scientific conferences and workshops * Preparing scientific manuscripts and publications * Contribution to supervising Bachelor and Master's theses * Writing and submitting a doctoral dissertation at the end of the project Your profile * Master's degree or diploma in neuroscience, physics, biomedical engineering, computer science or similar fields * Interest in the topic of the project and in vision/neuroscience research in general * Sound knowledge in conducting (f)MRI experiments and analyzing (f)MRI data, preferably at ultrahigh magnetic field * Excellent programming skills (MATLAB, Python, Linux shell, etc.) * Excellent English skills * Excellent organizational, communication and social skills, independence, reliability * Preferably sound knowledge of the visual system More information is available at https://secure-web.cisco.com/1QSEqOWvfyj3Fn-k_qchrTdPC3oPy2SGg1xDUvzx9ueGD8… , http://secure-web.cisco.com/13ejGmNm191wKTEtay0FeS3AMK97XGb6RNkQtfnvjwL2i2Z… and https://secure-web.cisco.com/1Fhf-9nVXOL71lbQuy8a0pzO-PeLa-akgsFsMyolBxJ-LY… Salary Salary scheme is according to the FWF scale for doctoral candidates. The minimum salary according to the FWF is currently EUR 2,684.10 gross/month. Expected position start: 1.10.2024 (negotiable) Application will be accepted until 13.07.2024 or until the position is filled. Application documents: * Motivation Letter * CV * Relevant diplomas/graduation certificates with grade transcripts * Contact information of two referees who would be willing to provide a reference letter upon request Application documents should be sent to Natalia.Zaretskaya(a)uni-graz.at<mailto:Natalia.Zaretskaya@uni-graz.at> -- Ass.-Prof. PD Dr. Natalia Zaretskaya Department of Psychology, University of Graz BioTechMed-Graz Universitaetsplatz 2 8010 Graz Austria +43 316 380 - 5117 natalia.zaretskaya(a)uni-graz.at<mailto:natalia.zaretskaya@uni-graz.at> https://secure-web.cisco.com/1QSEqOWvfyj3Fn-k_qchrTdPC3oPy2SGg1xDUvzx9ueGD8…

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Group Stats for hipposubfields, brainstem and amygdalar
by Carina Obermüller 21 May '24

21 May '24

External Email - Use Caution Dear Freesurfer team, I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent Freesurfer course, but I can’t find it anymore. Could you help me out? Also more generally, is there an overview page of all the possible group stats commands? Thank you so much in advance for your reply! Sincerely, Carina

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how to resolve recon-all stopping at fill step
by Dong, Yilei 20 May '24

20 May '24

External Email - Use Caution Dear FreeSurfer developers, Apologies for emailing once again about how to resolve the recon-all stopping exactly at the fill step. I understand this may have to do with specific issues on UCSD's computer cluster, but if UCSD's cluster is not having the most up-to-date version of the FreeSurfer module, would it make a difference if I asked UCSD's supercomputer team to update the module version, so that the entire processing stream may be able to run all the way for 1 subject? Would it also make a difference if I increased the number of cores for 1 subject from 1 to 2? Sincerely, Yilei

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Request to Edit Page (if possible)
by Emily Popa 19 May '24

19 May '24

External Email - Use Caution Hello, I hope all is great. I ran into many issues using the -make flag with V 7.1 (based on instructions found in https://secure-web.cisco.com/1-msyefLYicmgJRp4aaxIyvNgBvyxq1mdLLjw-c5oMGhWw…) and discovered after investigating erratic behavior/crashes across a bunch of re-processed cases that I had made edits to, that the functionality is no longer supported. I think it might be really helpful to others if at all possible to indicate this on the wiki where it is mentioned as it took some time to find the relevant post in the archives. Thanks! Best, Emily S. Popa, M.S. Programmer Analyst I, Neuroimaging Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center 1301 20th St. #250 Santa Monica, CA. 90404 (408) 750-7971 (M) [cid3519*image001.jpg(a)01D7EC78.96AA1AC0]<https://secure-web.cisco.com/1sywoT0V8YjrBxyLolh3M6xFLNeV0zhNs_KZrVKcDpGYsj…> [cid3519*image002.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/18aF2I8PTK20vtBR9E_9H31BpGDjhBCja4yiOh-QxkCRHq…> [cid3519*image003.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/1nP2xsoAmMqTxDrqwvMdo5_oVf0Rl3v064B9gfXlPnVOdK…> [cid3519*image004.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/13KwzPRLUTKRpKorxcfsWml1ZEQvZ0tCa1ePVRRywCMbm5…> [cid3519*image005.jpg(a)01D7EC78.96AA1AC0] <https://secure-web.cisco.com/1Ce1VlXCnx6O336wKEGQ3TzL8YB9U8VqME55UBddu-2hgp…>

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Freesurfer on a high-performance cluster (HPC) - MATLAB runtime
by Camilo Castelblanco Riveros 18 May '24

18 May '24

External Email - Use Caution Hi all, I hope your weekend is going great! *Context*: I am trying to run the amygdala/hippocampus segmentation in an hpc. *Issue*: The cluster that I use doesn't have the libmwlaunchermain.so file from MATLAB's 2019b runtime under (/optnfs/freesurfer/7.4.1/MCRv97/bin/glnxa64). Because I don't have permission privileges and standard bin/paths don't apply in the hpc, I can't do something like fs_install_mcr. *Question*: Does someone have the libmwlaunchermain.so file, or is there a way to run the amygdala/hippocampus module without it? Any experience with the hpc is helpful! With gratitude, Camilo ------------------------------------------------------------------------ *Camilo Castelblanco Riveros (He/His)* Integrative Neuroscience at Dartmouth (IND) Ph.D. Student Robertson Lab <https://secure-web.cisco.com/1J85yiocytHpTivZxcZMk7Vqi6lHw5Fk9k8jeONEsfXv5L…> & Bujarski Lab <https://secure-web.cisco.com/1yuSzZ9v0bN8y511sYU8prP1iK-NYHoAYmK7xdIhAPLC2a…> Diversity Student Advisory Board Member e: ccastelblanco.gr(a)dartmouth.edu <camilo.a.castelblanco.riveros.gr(a)dartmouth.edu> [image: Integrative Neuroscience at Dartmouth (IND) (@DartmouthNeuro) / Twitter]

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Post a Postdoctoral Scholars in Neuroimaging at the University of Miami Miller School of Medicine
by Otero Ospina, Andrea 17 May '24

17 May '24

External Email - Use Caution Hello Could you please post a job announcement for a Postdoctoral Scholar Position in Neuroimaging, at the University of Miami Miller School of Medicine, to your mailing list. I'm already inscribed in your mailing list. I'm attaching our post job! Best, Andrea Otero

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mri_watershed Error: read failed
by Schroder, Kirsten 16 May '24

16 May '24

External Email - Use Caution Dear Freesurfer developers, I am currently conducting a research project in which I am running 7T MP2RAGE images in Freesurfer version 6.0.1 but have a run into an issue. For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL region of the brain empty!” which I tried to fix using the -skullstrip -no-wsgcaatlas flag but get different results: 1 image was successful but for 2 images I get mri_watershed Error: read failed (see attachment). It appears that the last file created is the 001.mgz file hence there is no T1.mgz file created and Freesurfer therefore gives this error. I wanted to know if there is way to fix this as I have not been able to find a successful solution from the archive. I have also run the same dataset in Freesurfer version 7.2.0 and receive the same error for some scans. Any help would be appreciated. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux Thank you, Kirsten

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Valid options.txt file for mris_pmake (and maybe .dsh.yml too)
by Garikoitz Lerma-Usabiaga 16 May '24

16 May '24

External Email - Use Caution Hi list! I was reading the documentation on mris_pmake (by the way, it is outdated, the documentation still asks for --surface00, at least in 7.3.2), and I would like to have a valid options.txt file to make it work with dsh (a valid example .dsh*.yml would be greatly appreciated too. I want to speed up a simple vertex to vertex calculation, as Bruce said in an old thread, I am able to run it line by line but there is a lot of overhead reading the surfaces, so it would be great to just do the calculations. Thanks!! Gari

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Issue related to converting .nii.gz file to .mgz using FreeSurfer's mri_convert
by Tsigaras, Thanos 15 May '24

15 May '24

External Email - Use Caution Hello FreeSurfer Developers, I am using FastSurfer for this processing, but the issue is related to FreeSurfer's mri_convert function. I wanted to perform some manual segmentation edits on the "aparc.DKTatlas+aseg.deep.mgz" output file of FastSurfer. Since ITK-SNAP can't open .mgz files, I used the mri_convert function to convert the .mgz file to .nii.gz. I performed the edits and tried to rerun FastSurfer using the manually edited .nii.gz file. I got the error: "ERROR: Specified segmentation output and conformed image output do not have same file type. You passed --asegdkt_segfile directory/to/aparc.DKTatlas+aseg.deep.nii.gz and --conformed_name directory/to/orig.mgz. Make sure these have the same file-format and adjust the names passed to the flags accordingly!" So I used mri_convert once again to convert the .nii.gz file back to .mgz. When tried to rerun FastSurfer, I got the error: "You passed --surf_only or --no_asegdkt, but the whole-brain segmentation (directory/to/aparc.DKTatlas+aseg.deep.edited.mgz) could not be found." I also tried opening the .mgz edited file using MRIcron, but I get an error there as well: "Error: first value in a MGH header should be 1 (got 1) and data type should be in the range 1..4. (got 10)", which is not the case when I open the original .mgz file. The way I am using the mri_convert function is simply "mri_convert aparc.DKTatlas+aseg.deep.edited.nii.gz aparc.DKTatlas+aseg.deep.edited.mgz". I've searched the list and no similar errors have been reported. Please let me know if you need more details to help me troubleshoot this issue. For your time and help I would like to thank you in advance! Best regards Thanos Tsigaras ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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error using mri_em_register
by Michal Zamberg-Elad 15 May '24

15 May '24

External Email - Use Caution It does not create the nu.mgz file. Error logs are attached. The result is that when running recon all it cannot find the LH and RH files and then collapses. Darwin Kernel Version 21.3.0 iMac-Pro 21.3.0 Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64 Thank you, Michal

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