Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

creating a new atlas
by Gibson,Cierra N 03 Sep '21

03 Sep '21

External Email - Use Caution Hello Freesurfer developers, I am attempting to create a new atlas for the freesurfer software that would allow me to analyze rat brain MRI images. I saw on the SurfaceRegAndTemplates page that I need to register and create an inflated template, but I am having trouble understanding how to do that. Could you possibly help, please? Thank you, Cierra Gibson

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fs_install permission denied
by Junyeon Won 02 Sep '21

02 Sep '21

External Email - Use Caution Dear Freesurfer experts, I was tiring to install fs_install using the below command. cd $FREESURFER_HOME/bin && curl https://secure-web.cisco.com/186mRL7xDETIpN5cZS-wivuTmyhZn0PmwqT8bMpnWm3D4D… -o fs_install_mcr && chmod +x fs_install_mcr It showed an error message saying permission denied so I added sudo as suggested here. https://secure-web.cisco.com/1d_mS4e4I0j64PnpWDAM0mBO-6wAmGqcg5riZxWWy6VAP8… However, even after adding sudo in front, it shows the same error message. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2010 100 2010 0 0 17104 0 --:--:-- --:--:-- --:--:-- 17179 chmod: Unable to change file mode on fs_install_mcr: Operation not permitted Could you please let me know how to resolve this? Best, JW ᐧ

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recon-all Longitudinal processing (baseline on 1.5T; followup on 3T)
by Jayachandra Raghava 02 Sep '21

02 Sep '21

External Email - Use Caution Hello Experts, I am planning to run the longitudinal processing pipeline (Freesurfer version 7.1.1). But I have a few subjects who were scanned on different scanner field strengths at baseline and followup. For example : Baseline was scanned on a 1.5T Siemens Scanner Followup was scanned on a 3.0T Siemes Trio Scanner I am planning to 1) run the cross-sectional processing for baseline without the 3T flag 2) run the cross-sectional processing for followup with the 3T flag 3) then generate the unbiased template and longitudinally process all the time points without any special flags. Is this the best way to process such data? Please let me know if there are any additional flags in the longitudinal processing pipeline to accommodate Scanner/Field strength changes. Best wishes Jay

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question for FREESURFER
by hyeyoung park 02 Sep '21

02 Sep '21

External Email - Use Caution Hi, This is hyeyoung Park from Seoul National University in South Korea. I have one question about FREESURFER. I ran recon-all using terminal, and finally I got files such as aseg.stats and aparc.stats. For the next steps, I'd like to extract the measurements like thickness or volume from these files using the terminal or "freesurfer" package in R. But I don't know how should I do for the next steps. How can I get the measurements for several subjects in parallel? I hope you can help me. Thank you, Hyeyoung

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matlab runtime error
by Corinna Bauer 02 Sep '21

02 Sep '21

External Email - Use Caution Hi all, I ran a few subjects successfully through7.1.1, but when I got to check the surfs in freeview I get an error about the Matlab runtime libraries below. However, I already have those libraries and the 2014b runtime environment installed on my Ubuntu 18.04. freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5X11Extras.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Core.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Gui.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Widgets.so.5: no version information available (required by freeview) freeview: relocation error: freeview: symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference I also tried re-installing the 2014b MCR, but get this message: fs_install_mcr R2014b curl: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libcurl.so.4: no version information available (required by curl) curl: (48) An unknown option was passed in to libcurl Let me know how to best proceed. Thanks! Corinna

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Shiny new 7.2!
by Andy Worth 01 Sep '21

01 Sep '21

External Email - Use Caution Is it true that all that is needed for a new official FS docker container to come into existence is to merge pull request #866 <https://secure-web.cisco.com/10DeE1N6s0_SCCbPo6uqcazn6bfeF4GN2L9n26obY0mrz4…>? That would be so very nice. We like the official release! 4.1K pulls of previous versions on dockerhub can't be wrong. Kind regards, Andy Worth Senior Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1q0M-qEiBJlwu49m9WEWx5rGqctEdeZiwaiHNtscHhu8sb1…>

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The Department of Psychology (http://secure-web.cisco.com/1L2oUeS03j4UpCKska-6NzVcNYkUOi4t3lCF7-KCqRL2UzvmuNigg1dexCNUvuS4mfvbONgeHxSnKxGIQ8x58YQo5DFR7RHXerH4W09GqHKfZQm6exjszmcWP9RcfvGe6QsjzBR_NOGCfwUDPHEXauO-vooHLHnSHsnBl0DE_6eQwpeTB9mxwA1WkCUlTXvJd7n89LG4mVwuLdW3r6yj8elx_mQ5tRw3dMvv5Ci8n5zESv2W6U-5I_Vk1V7Fr5gCBRcbgCFmnKzV4-pPB1cl4KA/http%3A%2F%2Fwww.psychology.umd.edu) at the University of Maryland, College Park seeks candidates for positions in Cognitive Neuroscience, Behavioral Neuroscienc
by Tracy Riggins 01 Sep '21

01 Sep '21

External Email - Use Caution Please post/circulate as appropriate; excuse cross-postings. Thank you. The Department of Psychology (http://secure-web.cisco.com/1L2oUeS03j4UpCKska-6NzVcNYkUOi4t3lCF7-KCqRL2Uzv…) at the University of Maryland, College Park seeks candidates for positions in Cognitive Neuroscience, Behavioral Neuroscience and Clinical Psychology with a starting date of August 2022. The full position announcements and application portal can be found via the employment links below. Assistant Professor in Cognitive Neuroscience https://secure-web.cisco.com/1Z-RRqxsigDpJer5hEkiA6TXEl0hLo4gO1jaUmugWYbggx… Assistant Professor in Behavioral Neuroscience https://secure-web.cisco.com/1kfG6aV4cfooPw7PvLEfDJPvEr2TvVbWiuQYrplqlgnG-v… Assistant or Associate in Clinical Psychology https://secure-web.cisco.com/1eMqsqMGPvfaje54pwO0AmenI9qYEC3SQoGp5sMXsDAAki… Application materials should be submitted through the link above no later than November 1, 2021 and should include: a cover letter, CV, statement of current and future research interests and research philosophy, a statement of teaching philosophy and experience (including evidence of teaching excellence, if available), and contact information for three references. Applicants should provide sample research manuscripts or journal articles in the Supplemental Document 1 field in eJobs. Because the Department of Psychology is committed to increasing the diversity of the campus community and promoting inclusion across campus, materials should address how the candidate will contribute to fostering a diverse and inclusive community. In addition, the Department embraces the values of open and reproducible science, and candidates are encouraged to address how they have pursued and/or plan to pursue these goals in their work. The University of Maryland, College Park, an equal opportunity/affirmative action employer, complies with all applicable federal and state laws and regulations regarding nondiscrimination and affirmative action; all qualified applicants will receive consideration for employment. The University is committed to a policy of equal opportunity for all persons and does not discriminate on the basis of race, color, religion, sex, national origin, physical or mental disability, protected veteran status, age, gender identity or expression, sexual orientation, creed, marital status, political affiliation, personal appearance, or on the basis of rights secured by the First Amendment, in all aspects of employment, educational programs and activities, and admissions. The University of Maryland has made the safety of our students, faculty and staff, and our surrounding communities a top priority. As part of that commitment, the University System of Maryland (USM) recently announced that students, faculty, and staff on USM campuses this fall, including UMD, are required to be vaccinated against COVID. As a prospective and/or a new employee at UMD, you will be required to comply with the University’s vaccination protocol. Proof of full vaccination will be required before the start of employment in order to work at any University of Maryland location. Prospective or new employees may seek a medical or religious exemption to the vaccination requirement at return.umd.edu <https://secure-web.cisco.com/1-xn068vbthEknoIWbkAwOfUqSZoMUsHVaKbCBo2LvGMRk…> and must have an approved exemption prior to the start of their employment. -- Tracy Riggins, Ph.D. Pronouns <https://secure-web.cisco.com/1iLnmQ8Au0eEK07bg8TX8wCNei48kyu0pxlj6dnWl89JgT…>: she/her/hers Associate Professor of Psychology Secretary, Cognitive Development Society 4094 Campus Drive, Biology/Psychology Building 2147J University of Maryland, College Park, MD 20742 ***************************************************** Research info: http://secure-web.cisco.com/1zMjA3wZL1bVISPYhKnp3xSpIOD2J73ZxmIVu46ORRGV5GK… <https://secure-web.cisco.com/1WZVU5oCPDkWjiZlUnNI84I3BX2osoEnVHC_dKT8q5Mzle…> and https://secure-web.cisco.com/1WZVU5oCPDkWjiZlUnNI84I3BX2osoEnVHC_dKT8q5Mzle… Black lives matter in academia <https://secure-web.cisco.com/10nyNX_SDjMsD8Bk7H-wMu9C4SlBSvAEYdvOZdmE_hje2d…> LGBTQIA Ally <https://secure-web.cisco.com/1RCgvgN2MM72_6sY3jVkD_dxYTBgytophWKzs5G-vMmu31…> actions <https://secure-web.cisco.com/1RCgvgN2MM72_6sY3jVkD_dxYTBgytophWKzs5G-vMmu31…>

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Freesurfer September 2021