Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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Postdoctoral position: Neuroimaging, PCAN lab, University of Calgary, Canada, 2 years
by Alexandru Hanganu 16 Jun '21

16 Jun '21

External Email - Use Caution Dear All, The PCAN lab: http://pcanlab.ca has a two-year funded postdoctoral research fellow position under the supervision of Dr. Oury Monchi starting immediately to work on the following project: *Neuroimaging and other predictors of cognitive and neuropsychiatric evolution in Parkinson’s disease using multi-modal MRI imaging techniques and machine learning.* The project is funded by the Canadian Institutes of Health Research (CIHR) . It involves longitudinal analyses of cortical thickness, tractography and BOLD resting-state fMRI analyses and will benefit from collaborations with Dr. Alexandru Hanganu at the Department of Psychology of the University of Montreal. Other collaborators include Dr. Nils Forkert head of the Medical Imaging Processing and Machine Learning laboratory. A special focus will be given to the neural origins and predictors of Mild Behavior Impairment (MBI) in Parkinson’s disease in collaboration with Dr. Zahinoor Ismail who has led the development of the MBI-checklist. The project will make use of an existing longitudinal study containing structural, diffusion weighted imaging and functional MRI, neuropsychological and behavioural assessment, and genotyping at three time points. The PCAN lab has been a pioneer in using different neuroimaging techniques to study the origins and evolution of cognitive more recently neuropsychiatric deficits in Parkinson’s disease with the ultimate goal of early prediction of dementia in the disease. Other interests include the function and application of neuromodulation techniques such as transcranial magnetic stimulation, Transcranial direct stimulation and low intensity focused ultrasound. The PCAN Lab is located in the Healthy Brain Aging labs of the Hotchkiss Brain Institute part the Foothills Campus of the University of Calgary. The Foothills campus is home to the Seaman Family MR Research Centre which host a General Electric 3T research dedicated MRI scanner. Requirements of the position include a PhD in Neuroscience, biomedical engineering, biomedical sciences, or Psychology with experience in the analysis of one or multiple MRI neuroimaging techniques such as cortical thickness/volumetry (e.g. *Freesurfer, FSL*), functional connectivity (e.g. *PPI, ICA, graph theory*), diffusion weighted imaging (e.g. *Dipy, MRTrix, FSL*). Some fluency in computer programming (e.g. *Linux, Unix, MATLAB, or Python)* is also required as well as the ability to write scientific peer-reviewed manuscripts. Please send applications (Cover letter, CV, and the name of 2 references including current supervisor) to Oury Monchi: oury.monchi(a)ucalgary.ca

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Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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Parcellation Error Pre-Post Central Gyrus R but not L Hemisphere
by Fraser Smith 26 Apr '21

26 Apr '21

External Email - Use Caution Hi there I have a clear parcellation error with one participant who does look to have an atypical structure around the right post-central gyrus (looks split in two). Both the pre and post central gyri are shifted significantly backwards – but only for the right not the left hemisphere. I see this has been mentioned before in the archives – but I have been unable to find a fix for this. Could you provide any tips on what to try? I am using v6.0.0. Best wishes Fraser Smith

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Failed tissue type check {Disarmed}
by Julie Ottoy 15 Apr '21

15 Apr '21

External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got the following error in only one of my subjects. When I ran the same subject with PVC and specified psf, it did run fine. $Id: mri_gtmpvc.c,- setenv - cd - mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o /gtmnopvc.output.ceregrey --rescale 8 47 sysname Linux hostname - machine - user - vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory /gtmnopvc.output.ceregrey Loading seg for gtm /ID/mri/gtmseg.mgz Loading seg ctab /ID/mri/gtmseg.ctab Reading /ID/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check Any suggestions would be appreciated! Thank you, Julie Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGD…> 2017-11-25 <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Douglas Greve <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV…> sorry, can you send me the details again? On 11/21/17 10:24 AM, Klein, Gregory wrote: Hello Donatas and Douglas, Did you ever find a cause and solution for this problem? I too occasionally get this error message, and cannot get the results of mri_gtmpvc for certain subjects. Any suggestions are welcome. Thanks, Greg -- Gregory Klein, PhD Principal Scientist, Biomarker Experimental Medicine Leader F. Hoffmann-La Roche Ltd. Bldg 01, Floor 16, N445 Grenazacherstrasse 170, 4070 Basel, Switzerland Mobile: +41 79 572 97 89 Office Phone: +41 61 682 07 59 email: gregory.kl...(a)roche.com Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City, AL7 1TW Registration No:100674 Confidentiality note: This message is intended for the use of the named recipient(s) only and may contain confidential and / or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 Partners Compliance HelpLine athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1vNIDvkxU5C3l-uZggX6Oz-MWAWokjyVkJCUVlEhq9XKRo…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Douglas N Greve <https://secure-web.cisco.com/1M-leUu9vjxLEhQIgnl6dfbF3d7ST4-ULxvVl3JoB7UDa6…> Donatas, please remember to include previous correspondence so that we have everything in one email. Can you upload your freesurfer subject so that I can debug it further? upload to https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r6… On 11/09/2016 12:17 PM, Donatas Sederevicius wrote: > > I followed the processing workflow as described in PETSurfer wiki > and gtmseg.mgz was created using gtmseg script as described. I > ran this processing for over 100 subjects and only one has failed. > > > > ___ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-… -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://secure-web.cisco.com/1ThbUNbSt9_UBVJvAmBRnAaRfVWyZ0ej5JxRkdyy8xuH36… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 Partners Compliance HelpLine athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1yv39xApOHJ3FS6xDcFycnMnbHtStZeNBiLl3QzfL8G4yu…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Donatas Sederevicius <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKl…> I followed the processing workflow as described in PETSurfer wiki and gtmseg.mgz was created using gtmseg script as described. I ran this processing for over 100 subjects and only one has failed. ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 Partners Compliance HelpLine athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1vPxlf-9EcToYjQ2NcohNFPvheryGJhjZq4nxdkmbOKRg2…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Douglas Greve <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV…> Was gtmseg.mgz created with the gtmseg script? On 11/9/16 4:43 AM, Donatas Sederevicius wrote: Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. Best regards, Donatas ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 Partners Compliance HelpLine athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1-KTvEDdAuFhtSF_p9XP0T2HYXV7p_VXGloR253IuV-slW…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Donatas Sederevicius <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKl…> Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. Best regards, Donatas ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 Partners Compliance HelpLine athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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TRACULA path error
by David Ziegler 26 Mar '21

26 Mar '21

External Email - Use Caution Hey Freesurfer folks, I'm running into a strange error with the TRACULA longitudinal stream, whereby all of the steps run "without error" but the final merged paths look like a collection of single voxels (see screenshot below). The individual paths typically show up as single or a few voxels as well. This seems to be happening on all/most of my subjects. I've checked the outputs from trac-all -prep and the FA volumes look right. I've also QAed all of the cortical surface recons and they look good. Also, the individual tract streamlines (the .trk files) look pretty reasonable (see second screenshot). So, I'm assuming that this is an issue at -path step when converting the .trk files to volumes, but am unsure how to troubleshoot it. I'm assuming that the path stats that are output are derived from the volumes and not the streamlines, so this is probably an important step to correct, right? Just FYI, I'm running freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on Ubuntu 18.04.4 LTS and FSL v4 (FSL v5.0 won't work with the trac-all -prep commands for me) and I run bedpost directly on the dmri folder (I have an SGE cluster). Any chance you've seen this error before? Thanks in advance for any advice! David merged path volumes: several of the streamline files from the same subject:

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-hires vs -conf2hires in 7.1.1.
by Alexopoulos, Dimitrios 21 Mar '21

21 Mar '21

External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Recon-all exiting with Errors during surface inflation
by Koch, Erin M. 01 Mar '21

01 Mar '21

External Email - Use Caution Hi all, The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug\" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log. This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 . As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now. Thank you for your help. Best, Erin

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label to surface
by Sam W 02 Feb '21

02 Feb '21

External Email - Use Caution Hi, Is there a way to convert a label file into a surface/overlay? Thank you! Best regards, Sam

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Freesurfer December 2020