Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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recon-all -s SOME_SUBJECT exited with ERRORS
by Emanuel Alvaredo 07 Nov '19

07 Nov '19

External Email - Use Caution Hello FreeSurfer Developers, I am running de following command /usr/local/freesurfer/subjects/SOME_SUBJECT /usr/local/freesurfer/bin/recon-all -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - all -parallel I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. I have checked the log but I dont find de cause. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks in advance Emanuel

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Help with "orig.mgz"
by Fernando Castellano 07 Nov '19

07 Nov '19

External Email - Use Caution good afternoon, I am using freesurfer for my thesis in image technician. I would like to know specifically what the orig.mgz file is? I have read that it is step 1 of re-conall. But I don't fully understand thank you, best regards

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Re: [Freesurfer] LME model contrast matrix (Diers, Kersten /DZNE)
by Liu Guodong 07 Nov '19

07 Nov '19

External Email - Use Caution Hi Kersten, Thank you so much for the reply and that helps a lot. There are still some questions that I hope you can help me. 1.For the first model in you last email, you said 'To get the mean for group B, one would need to add the beta weights of the two regressors.’. I wonder if the beta weights should be 1 for regressors1 and 1 for regressor2, and the mean for group B is regressor2 plus regressor1 with the condition the value of group B is bigger than group A. 2.Is there any P-value for the lme_fit_FS function to present the quality of the fitting? 3.As you said before, if I have 3 group A,B,C for this model, and group A is reference group, the regressor1 is the mean of group A, and regressor2 and 3 reflect the difference between group A and B,C. But if I want to know the difference between B and C, what should I do. From the F-test, there only have a P-value to reflect how different between group B and C, I wonder can I compute a value the same as regressor 2 to reflect the difference? Thanks! Best regards, Guodong > > ------------------------------ > > Date: Tue, 5 Nov 2019 09:48:06 +0000 > From: "Diers, Kersten /DZNE" <Kersten.Diers(a)dzne.de> > Subject: Re: [Freesurfer] LME model contrast matrix (Diers, Kersten > /DZNE) > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1572947286.4016.34.camel(a)dzne.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello Guodong, > > consider as an analogy a two-sample t-test, where we simply compare two > groups A and B: > > If formulated as a regression problem, a commonly used model matrix for > this test (but others are possible, too) will consist of two columns, > one being all ones (the intercept), the other being zero for group A > and one for group B. > > The beta value for the first regressor should reflect the mean for > group A (which is chosen as the reference group), and the beta value > for the second regressor should reflect the difference between group A > and B, which is the primary interest for this comparison. To get the > mean for group B, one would need to add the beta weights of the two > regressors. > > The LME design matrices follow the same logic. > > Alternatively, as said before, other design matrices are possible. In > the above toy example, one could also use a matrix with two columns, > where column 1 is one for group A and zero for group B, and column 2 is > zero for group A and one for group B, thus omitting the overall > intercept. Then, the beta weights would directly reflect the means of A > and B. To get the difference between groups A and B, one would need to > subtract the beta weights. > > Mathematically, the two above models are equivalent. This also implies > that one should not specify a model where there is an intercept, a > regressor for group A, and a regressor for group B, because in this > case, the regressors would be linearly dependent. Since having an > overall intercept is advantageous (especially in more complex modelling > situations than this toy example), the first model is the preferred > one. > > Hope this helps, > > Kersten > > > On So, 2019-11-03 at 16:33 +0800, Liu Guodong wrote: >> ????????External Email - Use Caution???????? >> >> Dear Kersten:? >> The ?1 and ?2 in the tutorial model is the regressing coefficients >> for all the subjects not only for the control subjects because all >> the intercept are one. I wonder why the reference group is control >> group in this case? >> >> Thanks in advance. >> >> Best regards, >> Guodong >>> >>> Date: Thu, 24 Oct 2019 08:06:28 +0000 >>> From: "Diers, Kersten /DZNE" <Kersten.Diers(a)dzne.de> >>> Subject: Re: [Freesurfer] LME model contrast matrix >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.ed >>> u> >>> Message-ID: <1571904388.10840.18.camel(a)dzne.de> >>> Content-Type: text/plain; charset="utf-8" >>> >>> ???????External Email - Use Caution???????? >>> >>> Hi Guodong, >>> >>> On Di, 2019-10-22 at 16:05 +0800, Liu Guodong wrote: >>>> >>>> ????????External Email - Use Caution???????? >>>> >>>> Hello FreeSurfer Developers, >>>> >>>> I'm doing the LME tutorial, and I have some questions . >>>> >>>> 1. Why don?t we need to put the healthy controls in the designed >>>> matrix X? >>> Because that would be mathematically redundant, given the intercept >>> and >>> the other group regressors.? >>> >>> In general, one chooses a reference group (in this case, controls), >>> and >>> this group is implicitly modeled (by the intercept). The other >>> group >>> regressors will then model the difference between that particular >>> group >>> and the reference group. >>> >>>> >>>> 2. What?s the interpretation of the first row of the contrast >>>> matrix >>>> [1 0 0 0 0], does it mean first group minus healthy group? >>> I assume that we are talking about the first example, i.e. the >>> simple >>> univariate case (not mass-univariate). >>> >>> Just to be precise, the first row of the contrast matrix would be >>> [ 0 0 0 1 0 0 0 0 0 0 0 0 0 0], right? >>> >>> The fourth regressor (which this contrasts tests) is "colum 3 * >>> time", >>> i.e. the interaction between the first group and time. This would >>> indicate to which extent the slope across time in this group is >>> different from the slope of the reference group. >>> >>>> >>>> 3. There is a pvalue and a vector sgn from the result of F-test, >>>> I >>>> know the interpretation of the sgn, but I don?t know the >>>> hypothesis >>>> of the pvalue, could you please help me with that? >>> Strictly speaking, we test (and try to reject) the null hypothesis >>> that >>> the ?parameter estimate (or a linear combination of parameter >>> estimates) is zero. >>> >>> Best regards, >>> >>> Kersten >>> >>>> >>>> Thanks in advance! >>>> >>>> Best regards, >>>> Guodong >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ------------------------------ >>> >> > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 189, Issue 5 > ******************************************

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