Freesurfer November 2019

freesurfer@nmr.mgh.harvard.edu

87 participants
122 discussions

T2 white matter surface refinement
by Defenderfer, Matthew K 11 Nov '19

11 Nov '19

External Email - Use Caution Hi, Looking through the documentation, there are extra options to include a T2 image to refine the pial surface boundary, but I was wondering if FreeSurfer can use a T2 in conjunction with a T1 to help refine the white matter/gray matter boundary? As in, gray matter with higher myelin content than average could cause the white matter boundary to be placed further out than normal when just using a T1; can FreeSurfer currently use a T2 image to help prevent that at all? Thank you -Matt Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology

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Longitudinal Analysis for functional connectivity data?
by Barbour, Tracy,M.D. 11 Nov '19

11 Nov '19

Hello Freesurfer experts! I see that there is a longitudinal processing pipeline for volume/cortical thickness. I was wondering if the same pipleline could be used for resting state functional connectivity based analysis? Best, Tracy

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mri_surfcluster error -- FsFastTutorialV6.0
by 王如雪 11 Nov '19

11 Nov '19

External Email - Use Caution Hi Sir/Madam: I got an error when executing the new version "mri_glmfit-sim" correction for multiple comparisons with permutation at the group level according to FsFastTutorialV6.0. This was the command I used: "mri_glmfit-sim --glmdir my-glm --perm 1000 1.3 pos --cwp .05 --2spaces" But it prompted: mri_surfcluster: could not read surface /home/freesurfer/subjects/fsaverage4/surf/lh.white No such file or directory after "mri_glmfit simulation done" However, I've verified that /home/freesurfer/subjects/fsaverage4/surf/lh.white existed and that I had read permission to it. And after I loaded it with freeview -f /home/freesurfer/subjects/fsaverage4/surf/lh.white, the lh.white file was opened in the freeview window while the command line prompted "Did not find any volume geometry information in the surface". Can you help me with this error? Thank you very much! Best, ---------------- Ruxue Wang PhD Student, Tsinghua University

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nuisance factors
by Georgina Angelopoulou 11 Nov '19

11 Nov '19

External Email - Use Caution I am sorry, please let me rephrase. I want to compare patients vs controls in Surface area and grey matter volume. I have already checked age slope and it is not significant for either GMV or SA. However eTIV slope is significant in both cases (we do check for eTiv slope first as we did for age, right?) So in that case that we have two nuisance variables (age and eTiv), eTIV is significant but age isn't, how are we going to formulate the contrast? Would 1 -1 0 0 0 0 be correct? Thanks once again, Georgina

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Post-doc position in fMRI research available at karolinska institute
by Erik Lindberg 11 Nov '19

11 Nov '19

External Email - Use Caution Hi we are looking for a new post-doc in neuroimaging at Karolinska Institutet at the Department of NVS. The Department of Neurobiology, Care Sciences and Society (NVS) conducts world leading research in aging, dementia, epidemiology and care sciences. For this position we are looking for someone that has experience in analyzing functional magnetic resonance images. Working with resting-state and experimental fMRI will be the applicants main duty in this project. The applicant may also work with different imaging modalities such as structural, diffusion tensor- and functional magnetic resonance imaging (fMRI) and its applications to Alzheimer’s disease and frontotemporal dementia. In particular, the person is expected to take an active role in applying advanced imaging methods. There are also possibilities to initiate individual research projects, based on the person´s interests and in collaboration with the University of Gothenburg. The successful candidate should show a high level of independency, be able to work in a team and be willing to supervise students. Further information can be found at: https://ki.varbi.com/se/what:job/jobID:295452/type:job/where:4/apply:1

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4d nifti probabilistic atlas of Thalamic Nuclei and Brainstem sub structures
by Mageshwar Selvakumar 11 Nov '19

11 Nov '19

External Email - Use Caution Dear all, I am interested in the probabilistic thalamic nuclei atlas and the brainstem substructure atlas. I downloaded the beta version of freesurfer to get acces to them, however i only see the thalamic nuclei one. Furthermore, Is there a way to convert the meshes into a 4d nifti probabilistic atlas. Or does someone already have a nifti that i could have access to? Thank you for your time 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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Brain connectivity postdoctoral position @ CIMeC University of Trento, Italy
by Jovicich, Jorge 11 Nov '19

11 Nov '19

External Email - Use Caution POSTDOCTORAL RESEARCH FELLOW (call open till December 6, 2019) - Development, testing and validation of MRI microstructural and functional connectivity methods to advance human neuroscience. - Center for Mind/Brain Sciences (CIMeC), University of Trento, Italy. - More details in the link below. Feel free to contact me for further information. Call Outline: https://r.unitn.it/en/cimec/mri/opportunities Application: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019a Best, Jorge -- Jorge Jovicich, Ph.D. Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Re: [Freesurfer] Spammer Error upon License File Generation
by fsbuild 10 Nov '19

10 Nov '19

External Email - Use Caution Hello Frederic, Please verify that you tried the steps below.  You could also try using an email address you have not previously entered into the system. - R. - - - - - I went to the following link,http://surfer.nmr.mgh.harvard.edu/registration.html And filled out the form ... under name fill in:titleFirstLast Under name of institution fill in:Institution Select type of institution that will use this software:Check box Under Your email address fill in:email address Under mailing address fill in:StateZipCountryTel Select operating system:Check box - then scroll down to the very bottom of the page and check the box[I agree] Then the web page should re-load to display: FreeSurfer RegistrationThank you for registering. Your FreeSurfer license XXXXX has been emailed to XXXXXXEmail fsregister(a)nmr.mgh.harvard.edu if you have problems with the attached license Then a few minutes later you should receive the “license.txt”  file which should be copied into the directory you have set as $FREESURFER_HOME in your shell environment. On Nov 10, 2019, at 14:36, Frederic Hopp <fhopp(a)ucsb.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Devs, after trying to run freesurfer w/ fMRIprep, I get the following error:--------GNU libc version: 2.23ERROR: Systems running GNU glibc version greater than 2..15  require a newly formatted license file (it's free). Please  download a new one from the following page:  http://surfer.nmr.mgh.harvard.edu/registration.html-------… which I tried to generate a new license via the above link. However, the form always redirects to a Spammer page. While I did generate a license file in the past, I would like to have an updated license compatible with the above system. I am not a spammer, but a PhD student at UC Santa Barbara :) Thank you! Best,--Frederic R. Hopp PhD Student -- UCSB Department of CommunicationResearcher -- Media Neuroscience Labfhopp.github.io_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Spammer Error upon License File Generation
by Frederic Hopp 10 Nov '19

10 Nov '19

External Email - Use Caution Hello FreeSurfer Devs, after trying to run freesurfer w/ fMRIprep, I get the following error: -------- GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------- After which I tried to generate a new license via the above link. However, the form always redirects to a Spammer page. While I did generate a license file in the past, I would like to have an updated license compatible with the above system. I am not a spammer, but a PhD student at UC Santa Barbara :) Thank you! Best, -- Frederic R. Hopp PhD Student -- UCSB Department of Communication <https://comm.ucsb.edu/> Researcher -- Media Neuroscience Lab <https://www.medianeuroscience.org/> fhopp.github.io

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Version 5.3 vs. Version 6
by Larissa Bechtle 08 Nov '19

08 Nov '19

External Email - Use Caution Hey everybody, i have a question concerning version 5.3 and 6.0 of freesurfer. Originally I used 5.3 for volumes and thickness as well as for a group analysis. Later I used 6.0 for an anatomical ROI Analysis. I read online that doing so should be okay but wanted i wanted to make sure that this is really the case. I am thankful for any answer! Best wishes Larissa

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Freesurfer November 2019