Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

Regarding xhemi comparison of hemispheres of the same subject
by Ghassemieh, A. (Anna) 15 Apr '21

15 Apr '21

External Email - Use Caution Dear all, I'm currently working on comparing left with right hemisphere activation for individual subjects and using version 7.1.1. Since it is on an individual level, we would like to register the left hemisphere of each subject to their mirrored right hemisphere (or vice versa). When looking at the way this is described in the wiki (https://secure-web.cisco.com/1b80Mej4E9rovgmSCJq2Tz2wDNVe2geAoqeHRggKKORugG…) we started to wonder the following: It is suggested to register to the symmetrical template for each subject. However, it is unclear to us why this is necessary since there is already a matched registration via the spherical reg file for each subject. Does anyone know if it is possible to use this for the purpose somehow instead? Kind regards! ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Skull stripping with T2
by Rohan Bareja 15 Apr '21

15 Apr '21

External Email - Use Caution Hello, I am doing skull stripping with free surfer v6.0, and have tried various watershed cut-offs to do skull stripping on T2 scans. But, it removes a lot of brain portion. Here are my commands: mri_convert /Applications/freesurfer/subjects/patient_20_t2/mri/T2_age_reg_bias.nii.gz /Applications/freesurfer/subjects/patient_20_t2/mri/001.mgz recon-all -s patient_20_t2 -autorecon1 ## to be used only when increasing or decreasing threshold of skull stripping. recon-all -skullstrip -wsthresh 25 -clean-bm -s patient_12_t2 Is there any way that I can improve upon this and get better results if I am missing something? Thanks, Rohan

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Re: [Freesurfer] retaining label ids
by miracle ozzoude 15 Apr '21

15 Apr '21

External Email - Use Caution [image: image1.png] [image: image2.png] Hello Doug, Thanks for the reply. I've a parcellation of the gm and wm with different label ids (see screenshot 1). I did like to extract a *non-binarised* wm to look like screenshot 2. mri_extract_label and mri_binarize don't keep the different colours. Is there a freesurfer command to achieve this? On Tue, Apr 6, 2021 at 2:07 PM miracle ozzoude <miracooloz(a)gmail.com> wrote: > Hello Doug, > > Thanks for the reply. > > I've a parcellation of the gm and wm with different label ids (see > screenshot 1). I did like to extract a *non-binarised* wm to look like > screenshot 2. > > mri_extract_label and mri_binarize don't keep the different colours. > > Is there a freesurfer command to achieve this? > > Many thanks > [image: image.png] > [image: image.png] > > On Tue, Apr 6, 2021 at 12:07 PM miracle ozzoude <miracooloz(a)gmail.com> > wrote: > >> Hello Doug, >> >> Thanks for the reply. >> >> I've a parcellation of the gm and wm with different label ids (see >> screenshot 1). I did like to extract a *non-binarised* wm to look like >> screenshot 2. >> >> mri_extract_label and mri_binarize don't keep the different colours. >> >> Is there a freesurfer command to achieve this? >> [image: image.png] >> [image: image.png] >> >> >> On Thu, Apr 1, 2021 at 2:00 PM miracle ozzoude <miracooloz(a)gmail.com> >> wrote: >> >>> Hello Experts, >>> >>> I did like to extract wm whilst retaining the label ids. I tried >>> mri_extract_labels but it didn't work. >>> >>> Any help would be appreciated. >>> >>> Many thanks, >>> Paul >>> >>

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Re: [Freesurfer] Install issue
by fsbuild 15 Apr '21

15 Apr '21

External Email - Use Caution Hello Pal, Could be because tar archive contains hard links - which I don’t believe are supported when running a linux VM on top of a Windows OS (error from the first hard link it encountered and tried to write - and then quit). You could try expanding the tar archive ignoring *all*links* with the following using the *star* (pre-cursor to tar) command (cut and paste below and change tar archive name if need be), $ star -x  f=freesurfer-linux-centos7_x86_64-7.1.0.tar.gz  -find ! -type l - R. On Apr 15, 2021, at 02:35, Pål Gunnar Larsson <pall(a)ous-hf.no> wrote:        External Email - Use Caution        Thank you for the response.The computer runs Win10 pro and are under AD-control. May be there are something there out of my reach. Funny that it is almost only unpacking of some man-pages giving errorsI’ll try your suggestions. Pål Dr. philos. Pål G. LarssonOverlegeNevrokirurgisk avdelingOslo UniversitetssykehusPostboks 4950 Nydalen0424 Oslo  Tlf.:  23074407Mobil: 93429791 E-mail: pall@ous-hf.no Denne meldingen innholder ikke sensitiv informasjon som bryter med Ous sine regler for taushetsplikt Fra: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] På vegne av Hoopes, AndrewSendt: 14. april 2021 19:42Til: Freesurfer support listEmne: Re: [Freesurfer] Install issue I’m not totally sure of the answer here. Could be filesystem limitations or a permissions issue. Have you tried untar’ing without the -p flag, or ensuring that you can write to /usr/local? BestAndrew From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Pål Gunnar Larsson <pall@ous-hf.no>Date: Tuesday, April 13, 2021 at 8:57 AMTo: freesurfer@nmr.mgh..harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Install issue        External Email - Use Caution        Today I tried to set up a new Freesurfer instance.It is on a Win10 system with Vmware 6.0 and Ubuntu 18 LTS. I have tried a local install and to /usr/local, but I get the same error  “cannot hardlink to….” And then a row of protocol errors (see attachment). What is the issue? Pål G. Larsson M.D., PhD.Department of NeurosurgeryDivision of Surgery and Clinical Neuroscience not sensitive _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Install issue
by Pål Gunnar Larsson 15 Apr '21

15 Apr '21

External Email - Use Caution Today I tried to set up a new Freesurfer instance. It is on a Win10 system with Vmware 6.0 and Ubuntu 18 LTS. I have tried a local install and to /usr/local, but I get the same error "cannot hardlink to...." And then a row of protocol errors (see attachment). What is the issue? Pål G. Larsson M.D., PhD. Department of Neurosurgery Division of Surgery and Clinical Neuroscience not sensitive

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New York City-based Neuroimaging Postdoctoral Position Available
by Sherry Simkovic 14 Apr '21

14 Apr '21

External Email - Use Caution The Psychiatry Research Institute at Montefiore Einstein (PRIME), a division of the Department of Psychiatry and Behavioral Sciences at Albert Einstein College of Medicine, is seeking a highly motivated postdoctoral scholar in the field of human neuroimaging. The focus of this position will be on analyzing fMRI data as well as related MR and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive science, radiology, engineering, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. Under the mentorship of Vilma Gabbay, MD, this postdoctoral scholar will be expected to advance both clinical and methodological knowledge through their postdoctoral training. Dr. Gabbay is the Director of Research at PRIME, a unique program in the greater New York metropolitan area dedicated exclusively to the study and treatment of adolescent mood and anxiety disorders, utilizing innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is dedicated to advancing the fields of magnetic resonance imaging and spectroscopy. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra, Philips Elition) with cutting-edge accelerated fMRI and edited MRS sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The primary responsibility for this postdoctoral fellow will be to analyze neuroimaging data from several ongoing and recently concluded research projects. Dr. Gabbay is fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. The initial employment period for this position is two years, with the possibility of extension. Salary will be competitive and commensurate with experience and the cost of living in New York City. Subsidized housing close to the Einstein campus in the Morris Park neighborhood of The Bronx is available. Please send a CV, statement of interest, and contact information for three references to Dr. Ely (benjamin.ely(a)einsteinmed.org<mailto:benjamin.ely@einsteinmed.org>) and Dr. Qi Liu (qi.liu(a)einsteinmed.org<mailto:qi.liu@einsteinmed.org>). Albert Einstein College of Medicine is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Best and thanks, Sherry Sherry Simkovic Study Coordinator Psychiatry Research Institute of Montefiore Einstein (PRIME) Pediatric Mood and Anxiety Disorders Program (PMAP) 1225 Morris Park Avenue, Bronx, NY 10461 TEL: (718) 839-7504 FAX: (718) 839-7575 EMAIL: sherry.simkovic(a)einsteinmed.org<mailto:sherry.simkovic@einsteinmed.org> [cid:image001.png@01D62891.B16B0C40]

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Freeview does not open files through the Freeview window (Terminal only)
by Max Korbmacher 14 Apr '21

14 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to open files through Freeview v.2.0 (I’m using freesurfer-i386-apple-darwin11.4.2-stable6-20170119), but cannot do it “manually” but only through scripting / the terminal. The operating system is macOS BigSur 11.2.3 (20D91). The latest attempt to open files this way have led the program to crashes or freeze. Please find attached an error report from the program crashing. Best, Max

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perl version needed for FS5.3
by Saemann, Philipp 14 Apr '21

14 Apr '21

External Email - Use Caution Hi all, we have problems in launching the recon-all command of FS5.3 (needed for a reconstruction of old results): during the nu_correct command various perl commands are called with a fix #!/usr/bin/perl -w The primary error is some "Can't used 'define(@Array)'. A bit of search showed that this seems perl version issue. Up to versio 5.18 this only seems to produce a warning, but no fatal error. On the respective node of our cluster we have installed another perl and call this module before, so the "which perl" correctly points to that perl main function. Still, errors appear, e. g. cannot locate MNI/Startup.pm, so obviously some packages are not correctly linked. What is the Installation recommendation on a Linux 64 Bit System to maFS5.3 compatible with the local perl? Best, Philipp

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Re: [Freesurfer] striatal parcellation
by Marques Ana-raquel 14 Apr '21

14 Apr '21

External Email - Use Caution ? Dear Freesurfer Team, we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation. We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz. However, we can't find how to perform this parcellation, and how to add it to the recon all steps? Thank you very much for your help! ? Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques(a)chu-clermontferrand.fr<mailto:ar_marques@chu-clermontferrand.fr> TEL: 04 73 751 600 FAX: 04 73 751 596

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mris_label2annot - make all command exiting with errors
by Marion DURTESTE 14 Apr '21

14 Apr '21

External Email - Use Caution Dear FreeSurfer developers, When running RECON-ALL -MAKE ALL after correcting a few errors from the recon-all output, it exits with an error. This occurs when the mris_label2annot command is called. > Loading /Users/mariondurteste/Documents/PhD/FreeSurfer/ReconstructedAfterQC/ToDo/ALA076_1/surf/lh.orig > 1 1376057 FG1 > 2 16711935 FG2 > ERROR: lh.FG2.mpm.vpnl.label, n=580, vertex 119494 out of range If we rerun the -make all command a second time it then finishes without errors. Do you know why this is ? * FREESURFER version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 * Platform: macOS BigSur 11.2.2 Thanks for your help ! Marion D

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