Freesurfer

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Error during processing. mris_make_surfaces(10174, 0x7fffbf9553c0) malloc: *** error for object 0x2431900024317: pointer being freed was not allocated/
by Троицкий Антон Александ рович 27 Sep '19

27 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, during the processing of patient data an error occurred. I don’t clearly understand a reason for this error. Technical description of this error is mris_fix_topology(5832,0x7fffc83843c0) malloc: *** error for object 0x7fcf88f2ca50: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug 0 defective edges Abort Darwin mac-2ap023-2.fccho-moscow.ru<http://mac-2ap023-2.fccho-moscow.ru> 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64 recon-all -s 2019-09-03_3DBrainView_T1_FSSD_2019-09-26_13-11 exited with ERRORS at Thu Sep 26 17:43:07 MSK 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting My assumption is that the error associated with memory allocation and its reading. Is there any suggestion about why it happened and how can I prevent it in the future? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0 2) Platform: macOS Sierra 10.12.6 3) uname -a: Darwin mac-2ap023-2.fccho-moscow.ru<http://mac-2ap023-2.fccho-moscow.ru> 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached

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Add email to post in mailing list
by Paula Reyero Lobo 27 Sep '19

27 Sep '19

External Email - Use Caution prl.sahelices(a)gmail.com

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Hippocampus Subregion
by ZZY 26 Sep '19

26 Sep '19

External Email - Use Caution Dear Freesurfer experts,                I got the volume of hippocampal subregions by using the command -  "recon-all -all -s bert -hippocampal-subfields-T1" in Freesurfer. How do I get the surface-level metrics of the hippocampal subregions (e.g., area, thicknness and curve) in the T1 mage? Best, Zhiyong

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Brainhack Global 2019: Call for Local Event Site
by brainhack org 26 Sep '19

26 Sep '19

External Email - Use Caution Dear colleagues, Brainhack Global 2019 will take place between *13-17 November*, and we are collecting interests from all possible sites. As each year we would like to host many Brainhack events all around the world to bring together initiatives and celebrate the power of collaborative and open science across the globe! Brainhack events aim to include: - tutorials on the use of open science tools, resources, and specific data analysis techniques that facilitate the reproducibility, openness, and collaboration of the neuroscientific investigations; - pitching and working on projects that support collaborative and rapid creation of tools; - keynotes from experts in specific research domains; - broadcasting tutorials from event sites; - unconference sessions that allow a relaxed and friendly environment for attendees to share their expertise; - social networking activities. If you are interested in hosting a local Brainhack event, please fill and submit the application form from here to get started: http://www.brainhack.org/global2019/#host. We have a team of eager researchers waiting to help you to organize a successful event in your local institute and town. For more details and information, please check the Brainhack Global 2019 website, follow the Twitter account and join the Mattermost channel: http://www.brainhack.org/global2019/ https://twitter.com/brainhackorg https://mattermost.brainhack.org/brainhack/channels/brainhack-global-2019 *Important Dates* *13 November 2019 Host confirmation* *13-17 November 2019 Brainhack events* We look forward to hearing from you, *The Brainhack Global 2019 Organizing Committee* Cameron Craddock, The University of Texas at Austin Dell Medical School, Texas, USA Pierre Bellec, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Canada Daniel Margulies, CNRS, Paris, France Isil Poyraz Bilgin, The University of Reading, Reading, UK Sofie Van Den Bossche, Ghent University, Ghent, Belgium Damion Demeter, The University of Texas, Texas, USA Anibal Sólon Heinsfeld, The University of Texas at Austin Dell Medical School, Texas, USA Peer Herholz, Montréal Neurological Institute & Hospital, McGill University, Montréal, Canada Jon Haitz Legarreta, Université de Sherbrooke, Sherbrooke, Canada

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Hippocampal Subfields Atlas
by ZZY 25 Sep '19

25 Sep '19

External Email - Use Caution Dear  Doug，      I have a group of multimode MRI data, including functional MRI, T1WI and diffusion MRI. We want to analyze the functional and structual connectivity between the hippocampal subregions.  Now, we have obtained individual-level atlas of hippocampal subfields for each subject by using FREESURFER 6.0 on the T1 image. What should we do next step? How do get a group-level atlas of hippocampal subfields and apply it to functuional and diffusion data?   Best, Zhiyong

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Color scale in TkSurfer and Freeview
by Zhi Li 25 Sep '19

25 Sep '19

External Email - Use Caution Dear Freesurfer experts, May I ask how could I customize the color scale in TkSufer? The default heat scale is blue-red. Could I change it to other colors, such as green-yellow or blue-white-red (like gradient)? Now I know how to customize the color scale in Freeview. The problem is in the 'custom' of Freeview I can not ignore zeros. Actually I'd like to display deactivation/negative value in 'light bule-white', activation/positive value in 'white-light red'. Any suggestions would be much appreciated. Best, lizhi

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Freesurfer vs. CAT12
by Maximo, Jose Omar 25 Sep '19

25 Sep '19

External Email - Use Caution Hi, Recently, I ran an analysis on Freesurfer and found increased cortical thickness on the patients compared to controls. Then, I heard about CAT12 and wanted to see if my results would be robust enough and be replicated using this other software. When I ran the analysis on CAT12, the results look completely different (both increased and decreases). I was not able to see the same clusters on the CAT12 results. I used the same subjects and covariates. I ran recon-all using both T1 and T2 images, whereas in CAT12 you can only use T1 images. Has anyone experimented with both software before? Best, Omar

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issue with lesions
by Sam W 25 Sep '19

25 Sep '19

External Email - Use Caution Hello, I have run recon-all on T1 scans of patients with WM lesions. I noticed however that for some patients the lesion is excluded from aparc.a2009s+aseg.mgz but for other patients it is included (and labelled as non-lesion). Ultimately I'd like to extract a) volume information in WM and b) volume information of the WM lesion. I think I can get the the WM volume from the wmparc.stats file. For the lesion volume I think I can take the WM-hypointensities from the aseg file right? However I noticed that if a lesion is on the right hemisphere, the Right-WM-hypointensities shows 0s in all columns, which cannot be right. I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in anatomical space, can I use this mask somehow in FS to inform recon-all where the lesion occurs? Thanks in advance! Sam

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Unable to access previous email archives
by Mageshwar Selvakumar 25 Sep '19

25 Sep '19

External Email - Use Caution Dear Freesurfer community, I have not been able to access the mail archives this week. It redirects to Martinos Center and asks me for a NMR Login and password. Is this the same login details we used to subscribe to the mailing list? I tried but my details didn't work. Looking forward for your replies. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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Re: [Freesurfer] Command not found
by fsbuild 24 Sep '19

24 Sep '19

External Email - Use Caution Hello Samer, The git bash shell on Windows will not be sufficient to run freesurfer programs on Windows.  Freesurfer is supported on CentOs Linux, Ubuntu Linux and MacOS.  However, some folks use the Ubuntu shell as supported on Windows 10.  This does work once setup in Windows and after some packages have been added to the Ubuntu image.  I have not used the Ubuntu shell on Windows very much, but you can read about installing and using it via the links below. - R. http://www.techken.in/linux/how-to-run-gui-ubuntu-linux-in-windows-10/ https://christopher5106.github.io/admin/2018/02/02/configure-windows-10-for… Samer Muhareb September 24, 2019 at 13:37         External Email - Use Caution        Hello, I am having trouble adding Freesurfer onto my PC. I have the program downloaded, but when I attempt to input a command from the Freesurfer program, it tells me that my command was not found.  This is my first time downloading a program to use in the command line without it being done for me, so I am not super clear on how to go about solving this issue or may have missed a crucial step. I was suggested to add the program onto the path but I am not really sure how to do that.  Any ideas or suggestions will be very helpful! I am using git bash on my windows, if that is helpful Thanks for taking the time to look into this, it is greatly appreciated.  Best,Samer Muhareb  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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