Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Converting .label coordinates to MNI
by Berger, Joel 27 Sep '19

27 Sep '19

External Email - Use Caution Hi friendly Freesurfers, I have seen this question asked, but can't find the answer. When exporting a label from tksurfer for a particular ROI for a subject, the coordinates in the .label document don't match up with any of the coordinates I can view in tksurfer. Is there a way/formula to convert these easily, ideally into MNI coordinates? I tried loading the label into Matlab with freesurfer_read_label.m converting to Talairach with freesurfer_label2tal.m and then also converting those coordinates using tal2mni.m, but the Talairach or the MNI coordinates do not match with the Talairach/MNI coordinates shown for the corresponding vertices in tksurfer. Thank you, Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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TRACULA - input Nifti instead of DICOM?
by Daniel Callow 27 Sep '19

27 Sep '19

External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Which files do I need to mri_deface to anonymized a subject?
by Tim Schäfer 27 Sep '19

27 Sep '19

External Email - Use Caution Dear FS experts, I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all pipeline to a consortium server, and they require all data to be anonymized. I found mri_deface [1] and wondered which files I would have to apply it to, and whether there are any other things I should be aware of. So far, my plan is to use mri_deface to replace, for each subject, the following files in mri/: * orig.mgz * orig_nu.mgz * T1.mgz * rawavg.mgz It would also be an option to upload only a subset of all the files produced by FreeSurfer, but I do not know which files to exclude and include, so if you have suggestions for this, it would also be very welcome. I will also look at some public datasets to see how they did it. [1] https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Error during processing data. mris_make_surfaces 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 Dear Bruce, I don't’ know exactly what happened during the processing. I have 8 Gb of RAM of my Mac. When the freesurfer is working there is approximately 2 Gb free RAM. Unfortunately, I don’t know how to check the working of RAM and was there a memory overflow or memory leaking. It will be great If you could check my data. I want to mention that the same problem was with other data of the same patient. I have uploaded the patient data on my google drive account. So here you can download it https://drive.google.com/file/d/1Rx2HG2ZXTTphrYDMRwguOljz9T4K7av1/view?usp=…. The error appeared for data for 2019-07-22. But the same problem appeared for data for 2019-09-04. 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 I saw the system requirements for the freesurfer and there was a mention about 8 RAM. Is it a necessary amount of memory only for freesurfer or for PC station? Best regards, Anton Troitskii. Are you running out of memory on the machine? If not, and you upload the entire subject dir we will see if we can replicate and fix this problem. cheers Bruce On Tue, 24 Sep 2019, Троицкий Антон Александрович wrote: 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_make_surfaces(10174,0x7fffbf9553c0) malloc: *** error for object 0x2431900024317: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug 000: dt: 0.0000, sse=991989.1, rms=2.913 021: dt: 0.5000, sse=841468.7, rms=1.605 (44.916%) 022: dt: 0.5000, sse=803776.9, rms=1.267 (21.055%) rms = 1.24, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=793308.4, rms=1.242 (1.982%) Abort My suggestion 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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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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