Freesurfer

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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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Tracula Anlsysis
by A.R. Sekar 16 Jun '21

16 Jun '21

External Email - Use Caution Hello Experts, I am using Tracula to analyse the white matter tracts of the cerebellum. I saw that the atlas has the Middle cerebellar peduncle<https://secure-web.cisco.com/1RU8MdA4Yds_PepNEq52WWjK8jWdz6oYfoTgR9zPaeseQL…>, does it also have the other 2 major white matter tracts of the cerebellum: inferior (ICP), and superior cerebellar peduncles (SCP)? If not how can I go about using tracula for the analysis of these white matter tracts? Thanks for your help! Regards, Akila

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mri_mcsim error when building Monte Carlo on fsaverage5
by Øystein Sørensen 16 Jun '21

16 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to build my own Z Monte Carlo on fsaverage5, as described on the BuildYourOwnMonteCarlo tutorial (https://secure-web.cisco.com/1uikaYhiWSF4KzsQTXjySqLmwrS4IRC0PJ5sIbxRfHQXCe…) but I get a segmentation fault. As a reproducible example, the following command tries to compute 10 replications at FWHM=15 and save it in a subdirectory fsaverage5 of my current directory. $ mri_mcsim --o ./fsaverage5 --base mc-z --surface fsaverage5 lh --nreps 10 --fwhm 15 Issuing this command leads to a segmentation fault. The full output is in the attachment (mri_mcsim_error.txt), and here are the last lines before the error happens: Loading /Applications/freesurfer/7.1.1/subjects/fsaverage5/surf/lh.white group_avg_surface_area 84969.3 group_avg_vtxarea_loaded 1 Loading label file cortex Loading /Applications/freesurfer/7.1.1/subjects/fsaverage5/label/lh.cortex.label Segmentation fault: 11 Adding the «--debug» option gives no additional information. If I add the “—no-label” option, it works. However, I need those labels for later use in mri_glmfit-sim so that does not solve the issue. Using fsaverage6 instead works fine: “$ mri_mcsim --o ./fsaverage6 --base mc-z --surface fsaverage6 lh --nreps 10 --fwhm 15” gives no error messages. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1 2) Platform: macOS Big Sur 11.4 PS! I’m also aware that permutation testing is in general recommended rather than Z Monte Carlo simulations, but in this particular application the dataset is so large that permutation testing is likely not a viable option, due to computing constraints. Best regards, Øystein Sørensen, PhD Associate Professor in Statistics Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo http://secure-web.cisco.com/1WEu63aU9x0YgcndrjS1ZoT7n-mRQdI0c2tfDzloh2yF1pU…

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Re: [Freesurfer] TRACULA trac-all cores/threads
by Drucker, Daniel 16 Jun '21

16 Jun '21

> Hi Daniel - Can you track down which command does this? I suspect that it's something in the pre- or post-processing, because I haven't added multi-threading to the main TRACULA executables (yet). trac-all calls trac-preproc calls eddy_openmp Daniel

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Re: [Freesurfer] Error in freeview
by fsbuild 15 Jun '21

15 Jun '21

External Email - Use Caution Hello Swati, Please check you have you setup the freesurfer environment by setting the environment variable FREESURFER_HOME to where the freesurfer distribution is installed followed by source’ing either the bash or csh setup script.   You can see the commands for that here, https://secure-web.cisco.com/1pWXNrTwcNFgC7ksSikz4u20fb7za4hxJ3a… The freeview binary expects to live under <freesurfer_installation_directory>/bin with the libraries it needs under the parallel subdirectory <freesurfer_installation_directory/lib.  Otherwise it may not find libraries like the one you listed which should be under <freesurfer_installation_directory/lib/vtk - R. On Jun 15, 2021, at 13:48, Swati Banerjee <swati.banerjee29(a)gmail.com> wrote:        External Email - Use Caution        Dear I am getting an error using the freeview. Please help me to resolve this issue.freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directoryWith regards,Swati--    -_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Error in freeview
by Swati Banerjee 15 Jun '21

15 Jun '21

External Email - Use Caution Dear I am getting an error using the freeview. Please help me to resolve this issue. freeview: error while loading shared libraries: libvtkDomainsChemistry-7.1.so.1: cannot open shared object file: No such file or directory With regards, Swati -- -

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Job Opening at CUMC/NYSPI: Scanning RA Position
by Chrisanthopoulos, Marika (NYSPI) 15 Jun '21

15 Jun '21

External Email - Use Caution Hello all, The Clinic for Aging, Anxiety, and Mood Disorders (CAAM) at the New York State Psychiatric Institute/Columbia Medical Center is currently interviewing to hire a Scanning (MRI) Research Technician. Please view the job description and submit your application through this link<https://secure-web.cisco.com/1FLIsp1bq-6rAoLTU9CMzclsVcu_Zim13NYcs2HcA11QrB…> if you are interested in applying. Thank you, Marika Chrisanthopoulos Program Manager Clinic for Aging, Anxiety, and Mood Disorders (CAAM) Neurobiology and Therapeutics of Aging New York State Psychiatric Institute Columbia University Medical Center P: 646-774-8697 F: 646-774-8693

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which file is freesurfer autoseg result?
by 1248742467 15 Jun '21

15 Jun '21

External Email - Use Caution hello, FSI do the brain region parcellation, I have label(ground truth) for each subject. I want to use my own neural network segmentation results and Freesurfer automatic segmentation results comparison, to get a qualitative and quantitative results? Which file in the label folder is the result of automatic segmentation? And how do I get quantitative results? As seen in some articles, the result of automatic segmentation by Freesurfer is 84.39 for DICE and 85.19 for ACC.

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Re: [Freesurfer] T1 hippocampal subfields exited with ERRORS
by 林鈺庭 15 Jun '21

15 Jun '21

External Email - Use Caution Dear Eugenio, We checked the RAM setting of the Docker container and found it was default using 2GB RAM! Then we set the Maximum RAM up to 16GB and work all done!! Thank you for your patience helping so much! Wish you have a great day! Best regards, Josephine <freesurfer-request(a)nmr.mgh.harvard.edu> 於 2021年6月12日週六上午12:01寫道： > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1_MhR_xuFQQ6f3qyQNiH1uM9hERvO8xgb2j3Rov_l0il6h… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: T1 hippocampal subfields exited with ERRORS > (Iglesias Gonzalez, Juan E.) > 2. Open Position: Postdoc or PhD Student for Deep Learning based > Lesion Recognition in human MRI (Dr. rer. nat. Johannes Jungilligens) > 3. Finding equivalent vertices on fsaverage_sym lh and rh > surfaces (Tim Sch?fer) > 4. Re: memory allocation error (Bernardoni, Fabio) > 5. Issues with recon-all hanging (Michael Datko) > 6. Re: how to visualize statistical maps in FS7.1? > (Bernardoni, Fabio) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Jun 2021 11:52:08 +0000 > From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] T1 hippocampal subfields exited with ERRORS > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <2E162B79-9558-4942-8B6E-55A7B384D524(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Dear Josephine, > This is unusual. Could it be possible that you are running out of RAM > memory? Do you have 16GB or more available? > Cheers, > /Eugenio > > On 11 Jun 2021, at 01:39, ??? <ytlin923(a)g.ntu.edu.tw<mailto: > ytlin923(a)g.ntu.edu.tw>> wrote: > > > External Email - Use Caution > > Dear Developer and Eugenio, > > We encounter the error at the end of the analysis,it looks like this: > > Smoothing mesh collection with kernel size 0.750000 > .../usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: > line 40: 499 Killed > /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML S013 /data > 0.333333333333333333333333333333333333 > /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz > /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz > /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 > right L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr > /usr/local/freesurfer/bin/' 0 > Linux f8e6a6f8a44a 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 > x86_64 x86_64 x86_64 GNU/Linux > > T1 hippocampal subfields exited with ERRORS at Thu Jun 10 10:22:54 UTC 2021 > > I've attached the log file here, could you help us with this error? Thank > you so much! > > Best regards, > Josephine > > <hippocampal-subfields-T1.log>_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1_MhR_xuFQQ6f3qyQNiH1uM9hERvO8xgb2j3Rov_l0il6h… > >

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In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?
by 1248742467 15 Jun '21

15 Jun '21

External Email - Use Caution Hello, Fs  In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative？ by the way, how the mean curvature reflects the degree of fold? Since the mean curvature is a local measurement, does the mean curvature map reflects the fold degree? 

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