Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

data in folder 'stats'
by PATRICIO FELIPE RIQUELME 05 Jul '24

05 Jul '24

External Email - Use Caution Hi everyone. I just began to use freesurfer, and I wanna know if the data in folder 'stats', after recon-all processing, is normalized in a common space or if I need to correct it in an additional step. Thank you Patricio Riquelme Departamento de Tecnología Médica Facultad de Medicina Universidad de Chile

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[Call for Abstracts] - 3rd International Conference on the Ethics of Artificial Intelligence (3ICEAI) (19-25 September 2024)
by steven gouveia 04 Jul '24

04 Jul '24

External Email - Use Caution [Call for Abstracts] 3rd International Conference on the Ethics of Artificial Intelligence (3ICEAI) University of Azores, Ponta Delgada, São Miguel Island, Azores 19-25 September 2024 (19-20 Online, 23-25 in-person) About: The third edition of this conference will be organized into two distinct segments. The first segment, scheduled for September 19-20, 2024, will be conducted exclusively online, featuring virtual presentations. The second segment, taking place from September 23-25, 2024, will consist solely of in-person sessions. ETHICS OF AI AWARD 2024 (in-person talks only): The best-submitted abstract will receive the opportunity to deliver a special Award Talk similar to a keynote talk (note: the selected author will have the fee waived). Previous winner (2023): Dr. Cristina Voinea (The Oxford Uehiro Centre for Practical Ethics, Uni. Oxford). We're also proud to announce a publication partnership with Palgrave Macmillan. Selected papers presented at the conference will be considered (following a peer-review process) for inclusion in the Palgrave Handbook of the Ethics of Artificial Intelligence, which will be edited by Steven S. Gouveia. The community is invited to submit proposals in different research fields until August 1st, 2024. KEYNOTES SPEAKERS: * Sabina Leonelli holds the Chair of Philosophy and History of Science and Technology at the Technical University of Munich, where she is also Research Director of the Ethical Data Initiative. * Pekka Mäkelä is an is a Research Coordinator in the Helsinki Institute for Social Sciences and Humanities (HSSH) at the University of Helsinki and the co-leader of the RADAR Group. * Ariane Hanemaayer is an Associate Professor at Brandon University, Canada, in the departments of Sociology and Gender and Women's Studies, and Affiliate Scholar at the Max Planck Institute for the History of Science. * Raul Hakli is a university researcher in practical philosophy and co-leader of the RADAR group. * Eleanor Drage is a Senior Research Fellow at the University of Cambridge Leverhulme Centre for the Future of Intelligence. * Hasse Hämäläinen is AI Scientist at Mehiläinen, holding a PhD in Philosophy in Philosophy from the University of Edinburgh. * Veridiana Cordeiro is a sociologist, a Professor at the Department of Sociology at the University of São Paulo, and a research fellow at the Center for Artificial Intelligence (IBM-Sao Paulo Research Foundation). Topics might include (but are not limited to): 1. Algorithmic Fairness and Bia 2. Privacy and Data Protection 3. Transparency and Explainability 4. Accountability and Responsibility 5. Human Rights and Social Justice 6. AI in Healthcare 7. AI in Autonomous Systems 8. Ethical Frameworks and Guidelines 9. AI and Decision-Making 10. Ethics of AI in Public Policy 11. AI and Environmental Ethics 12. Ethical Education and Awareness 13. AI in the Workplace 14. Global Perspectives on AI Ethics 15. Emerging Ethical Issues in AI 16. AI, Aesthetics and Cinema 17. Other topics related. FEES: * Professionals (posdoc, professor, tenure-track): € 160,00 * Students: (Master, PhD): € 110,00 Languages of the colloquium: English and Portuguese. SUBMISSIONS: * IMPORTANT: you should clearly state if you are submitting for the online segment (OS) (19-20 September) or the in-person segment (PS) (23-25 September). If (OS), you need to provide a preferred time schedule considering the Azores Time Zone (UTC - 1 hour). In-person submissions have a higher chance of being accepted (more slots available); * Proposals should include two files: (in word. format): (1) a cover page with identification, academic affiliation, and title (2) an anonymized title and abstract (maximum 250 words) and sent to interconfethicsofai(a)gmail.com * Paper duration: 30 minutes (20 minutes presentation + 10 minutes for discussion); * Information: in order to facilitate the request for funding of the accepted talks so speakers can prepare their travel in advance, notification of acceptance or rejection will be given in a 7-10 days period after the submission is submitted (and reviewed); * Papers presented at the colloquium are expected to be published in several projects (volumes, special issues, etc.) (this is optional - more information after the end of the conference); * Any doubts or concerns can be addressed to: interconfethicsofai(a)gmail.com Venue: University of Azores | Address: Rua da Mãe de Deus, 9500-321 Ponta Delgada, São Miguel, Açores. Organization: Mind, Language and Action Group | Institute of Philosophy | University of Porto Center for Humanistic Studies | University of the Azores Organizing Committee Steven S. Gouveia (Chair) Rui Sampaio da Silva (Local Organizer) Sofia Miguens Jaroslav Malík Romeu Ivolela Liberty Severs Support: CEEC Project by FCT 2022.02527.CEECIND TL Modern & Contemporary Philosophy RG Mind, Language and Action Group (MLAG) Instituto de Filosofia da Universidade do Porto – UIDB/00502/2020 Fundação para a Ciência e a Tecnologia (FCT) Reitoria da Universidade do Porto + Center for Humanistic Studies University of the Azores

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LME longitudinal subcortical ROI analysis
by Dan Levitas 03 Jul '24

03 Jul '24

External Email - Use Caution Hello, I recently performed an LME longitudinal mass-univariate (surface) analysis and am now trying to do something similar, but with subcortical (aseg) ROIs instead. I first created an aseg table with the following command: * asegstats2table \ --sd $subjects_dir \ --qdec-long /path/to/long.qdec.table.dat \ --segno 4 10 11 12 17 18 26 43 49 50 51 53 54 58 251 253 255 \ --stats aseg.stats \ --tablefile $output_file* The LME tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) provides information and examples of both a univariate and mass-univariate approach. While univariate seems most appropriate in this case, the example details design matrix setup and testing of a single ROI (hippocampus), whereas I would like to assess several subcortical ROIs. Would I simply create a loop structure to set up design matrices for each ROI (both hemispheres) and test them individually, or can I perform a mass-univariate approach to assess all ROIs at once? Thanks, Dan

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Scanner and Freesurfer-version differences
by Bronwyn Overs 03 Jul '24

03 Jul '24

External Email - Use Caution Hi Freesurfer Mailing List, I work on a large bipolar disorder imaging study that has been running for over 10 years. We previously acquired 2 sMRI time-points (pre 2013, n ~500, n ~250 at each time-point) on a single Philips 3T scanner and these images were processed with Freesurfer version 5.3. We have just now acquired a third imaging time-point that was completed on a different scanner (Siemans, n ~120) using a different acquisition protocal. So I have three questions for the mailing list, that I'm hoping will inform the design of our analysis protocol: 1. Are there specific considerations for processing structural MRIs that have been acquired on different scanners and with different acquisition protocols? 2. Reprocessing all time 1 and time 2 images with a newer version of Freesurfer is a huge undertaking (for both processing time and personnel time required to review and edit). However, is there a reason why a newer version of Freesurfer should be used (e.g. publication considerations, more consistent output) as opposed to processing time 3 with v5.3? 3. I know there are differences in the output across different versions of Freesurfer. However, do different system set ups (e.g. linux, mac, as well as operating systems) have an impact on the output, even if the same version of Freesurfer is used? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Re: [Freesurfer] freesurfer as module
by fsbuild 02 Jul '24

02 Jul '24

External Email - Use Caution  My understanding is that it is up to the sysadmins who run a cluster to choose how to present and configure the apps they host whether it be thru modules, spack, or other tools.  We don't track how cluster admins do that, but you could ask the helpdesk for the cluster you are going to use (which presumably lists there is some version of freesurfer already available on the cluster).  Most have online documentation stating how to run their apps. I have used Freesurfer in the past on the SDSC cluster, and according to their web pages, they do use modules,https://www.sdsc.edu/support/user_guides/expanse.html#software - R. On 7/1/24 14:55, Dong, Yilei (yid025(a)health.ucsd.edu) wrote Hi Freesurfer Developers,  If Freesurfer is available as a module on a computer cluster, is it still necessary to source/configure the freesurfer module in a .bashrc script on Linux?  Sincerely, Yilei  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Freeview cannot be opened (MacOS)
by fsbuild 02 Jul '24

02 Jul '24

External Email - Use Caution   If you prefer to run the last stable release (7.4.1), then I suggest downloading and installing the Intel binary package installer, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-mac…  To bypass some security prompts, right click on the package file and then choose "open will default ..." You should check the path, but I think you would set things up in the (bash) shell as, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1... source the environment setup script ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh If you don't mind running the latest development build (which can be unstable), then you can try the native arm64 binary package installer via the link, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS… Install the same way via right click as listed above.  Then check the path, e.g, $ export FREESURFER_HOME=/Applications/freesurfer/dev... source the environment setup script  ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Assuming you have your license file setup, e.g., to be read via FS_LICENSE environment variable with license.txt under your home directory, $ export FS_LICENSE=$HOME/license.txt - then it should work to run freeview.  I would first try running freeview from the shell command line w/o any arguments to see if it opens an empty window.   $ freeview Then exit and try it again with a known to be good volume, $ freevivew $SUBJECTS_DIR/bert/mri/brain.mgz - R. On 7/1/24 13:42, Melih Keskin (keskinmelih07(a)gmail.com) wrote:         External Email - Use Caution         Hi, I am trying to open Freeview using my M1 Macbook (Monterey version 12.5). I am posting the error it gives me below. I followed the steps from the below thread but none of the solutions worked (mainly changing the privacy settings and getting a new Freesurfer license). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/… Is there a solution to this problem as of 2024? Thank you in advance,Melih 2024-07-01 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead.  [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run  [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a darwin12. named Melihs-MacBook-Pro.local by keskin Mon Jul  1 20:41:01 2024 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Calculating intensity of Individual voxel
by ERNEST KISSI 02 Jul '24

02 Jul '24

External Email - Use Caution Hi, freesurfer team Is there a way to calculate the intensity of a voxel.Let say, I have a voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be done in freesurfer?

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freesurfer as module
by Dong, Yilei 01 Jul '24

01 Jul '24

External Email - Use Caution Hi Freesurfer Developers, If Freesurfer is available as a module on a computer cluster, is it still necessary to source/configure the freesurfer module in a .bashrc script on Linux? Sincerely, Yilei

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Freeview cannot be opened (MacOS)
by Melih Keskin 01 Jul '24

01 Jul '24

External Email - Use Caution Hi, I am trying to open Freeview using my M1 Macbook (Monterey version 12.5). I am posting the error it gives me below. I followed the steps from the below thread but none of the solutions worked (mainly changing the privacy settings and getting a new Freesurfer license). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70979.html Is there a solution to this problem as of 2024? Thank you in advance, Melih 2024-07-01 20:41:03.731 Freeview[70874:2969887] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a darwin12. named Melihs-MacBook-Pro.local by keskin Mon Jul 1 20:41:01 2024 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

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recon-all is shutting down? because of flair?
by egemen gok 30 Jun '24

30 Jun '24

External Email - Use Caution *Hello Freesurfer Developers* recon-all is shutting down for some reason, this is the last lines of the code before shutting down. (It ran approximately 11-12 hours) and fyi = I used flair image because there was no T1 image of the patient [image: image.png] and this is the log file (recon-all.log) = [image: image.png]

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