Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

freesurfer output
by Z Hessam 14 Oct '17

14 Oct '17

Hello FreeSurfer Developers, I can't access numerical value of each volume after segmentation of MRI images. how can i access that? does "freesurfer" produce such value for each segment? Best, Hessam

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Errors on compiling FreeSurfer
by Aziz Nanthaamornphong 13 Oct '17

13 Oct '17

Hi Experts, I tried to compile FreeSurfer on Ubuntu 16. When I ran a command 'make check', I got these error messages: */usr/bin/ld: warning: libtk8.4.so <http://libtk8.4.so>, needed by /home/aziz/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets/libKWWidgets.so, not found (try using -rpath or -rpath-link)/usr/bin/ld: IconLoaderTest.o: undefined reference to symbol 'Tcl_GetStringResult'//usr/lib/x86_64-linux-gnu/libtcl8.4.so <http://libtcl8.4.so>: error adding symbols: DSO missing from command linecollect2: error: ld returned 1 exit statusMakefile:947: recipe for target 'IconLoaderTest' failedmake[2]: *** [IconLoaderTest] Error 1* Best Wishes, Aziz.

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mris_anatomical_stats: segmentation fault core dumped
by Keiko McCreary 13 Oct '17

13 Oct '17

Hello Freesurfer developers, After succesfully running two recon-all's (error free), the third failed during mri_anatomical_stats. Any help would be appreciated (I am new to freesurfer). I found this error reported but not when recon-all has already successfully ran. Linux xubuntu-virtual box Freesurfer v5.3 recon-all.log is attached Thank you, Keiko -- J. Keiko McCreary, PhD Postdoctoral Fellow SARTAN-AD Clinical Research Coordinator (Lethbridge Site) Canadian Centre for Behavioural Neuroscience University of Lethbridge Office: EP 1218 Phone: 403-394-3985 Cell: 403-393-0181 keiko.mccreary2(a)uleth.ca or @gmail.com

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cortical surface area
by Alexopoulos, Dimitrios 13 Oct '17

13 Oct '17

What measure is for the cortical surface area? The measure in the aparc.stats file states 'WhiteSurfArea' Jim ________________________________ 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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Qdec image considering multiple variables
by 박경일 13 Oct '17

13 Oct '17

Dear FS developer, I am a FS beginner and trying to make QDEC images of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.table.dat file. However, adding any other factors such as hypertension, diabetes... etc. made error messages in a terminal window. I guess this error came from the some blank data, because some subjects do not have any information regarding hypertension or diabetes. Is there a way to make a figure showing a results of multivariate analysis? Thanks a lot in advance. Kyung Il Park, MD

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Re: [Freesurfer] volume vs surface-based and surface smoothing
by Matt Glasser 12 Oct '17

12 Oct '17

Volume-based registration is fine with subject as you have the same brain that you are registering (ideally such registrations are 6 DOF rigid registrations and any image distortions are corrected for). Surface-based registration is better when comparing across subjects due to the variability in cortical folding patterns and locations of areas relative to folds across subjects. Smoothing is best done on the surface if it is done at all. Smoothing in the volume harms one¹s spatial localization precision much more than smoothing on the surface for an equivalent FWMH in mm. It is worth keeping in mind that smoothing on the surface does still blur across cortical areal boundaries, however, so for many analyses it may be better to average within cortical areas rather than to smooth a lot. Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Alissa Stafford <alissa.stafford(a)jhu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 12:29 PM To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] volume vs surface-based and surface smoothing Hello, I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess. Registration has 2 parts: 1: the native anatomical space is registered with the fsaverage space. This is happening during recon-all. 2: native functional data is registered with the native anatomical data. This is happening during register-sess in preprocess-sess. Aren¹t these both volume-based registrations? If not when are the surfaces created? My concern is that it is volume-based and I was under the impression from this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all registrations should be done on the surface. I am also confused about rawfunc2surf-sess. I believe up until this function in preprocess-sess, everything has been done in the volume so this is the first step that is done in the surface, is that correct? And then does this do smoothing? I realized it has a fwhm input option so it must smooth. So is this where the functional data is now expressed in the surface and it also smooths? Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess? I basically just want to be making sure I understand when registration is volume-based or surface-based and when it¹s appropriate to use volume-based. And I was using the rawfunc2surf function assuming it was for smoothing, but I am not so sure if this only creates the surface or also smooths. Thanks, Alissa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://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 at http://www.partners.org/complianceline . 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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R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 12 Oct '17

12 Oct '17

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B- Clusters in which the fMRI (dependent variable) is associated to the structural data (covariate), taking in account the groups (I suppose that the maps will be in the slope folder) ---> MANOVA between 4 groups Please could you check the contrast reported below? I suspect that there are some errors because, looking at results: The slope map is the inverse in color of the intercept map and the intercept did not correspond to the results which I obtain by using G4V0 C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25 C15) group.effect.intercept 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 C16) group.effect.slope 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 11-ott-2017 17.28 >A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance > >the rational is to make them sum to 1.0 so that the gamma.mgh file has >units of mm (or whatever the input units are). It is unimportant for >p-values. > > >On 10/10/2017 01:54 PM, stdp82(a)virgilio.it wrote: >> Thanks >> >> In which contrast I must change "1" with "0.25"? >> What is the rationale to use 0.25? >> >> >> Sent from Virgilio Mobile >> ________________________________ >> >> Il 10/10/2017, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> ha scritto: >> >> I don't understand what you mean by "where I should use" >> >> I thought I looked through all those contrasts a few weeks ago, no? >> >> >> On 10/10/2017 04:22 AM, stdp82(a)virgilio.it wrote: >>> You have suggested to use >>> 0 0 0 0 .25 .25 .25 .25 >>> to look the map where, considering the group differences, the covariate >>> predicts the dependent variable (functional connectivity) in 4GV1. >>> >>> Below I'm reporting the contrast that I have used. >>> Please could you check it and suggest correction? >>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please? >>> >>> Thanks >>> >>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>> C15) group.effect.intercept >>> 1 -1 0 0 0 0 0 0 >>> 1 0 -1 0 0 0 0 0 >>> 1 0 0 -1 0 0 0 0 >>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>> >>> >>> >>> >>> >>> >>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>> Thank you very much. >>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>> Which are the contrast reported below that I should modify? >>>> >>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>> C15) group.effect.intercept >>>> 1 -1 0 0 0 0 0 0 >>>> 1 0 -1 0 0 0 0 0 >>>> 1 0 0 -1 0 0 0 0 >>>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>>> ----Messaggio originale---- >>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>> Data: 9-ott-2017 22.56 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance >>>> >>>> I don't know what you are asking >>>> >>>> >>>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>>> Thank you very much. >>>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>>> Which are the contrast reported below that I should modify? >>>>> >>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>> C15) group.effect.intercept >>>>> 1 -1 0 0 0 0 0 0 >>>>> 1 0 -1 0 0 0 0 0 >>>>> 1 0 0 -1 0 0 0 0 >>>>> C16) group.effect.slope >>>>> 0 0 0 0 1 -1 0 0 >>>>> 0 0 0 0 1 0 -1 0 >>>>> 0 0 0 0 1 0 0 -1 >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> Data: 3-ott-2017 16.19 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance >>>>>> >>>>>> probably you want 0 0 0 0 .25 .25 .25 .25 >>>>>> >>>>>> >>>>>> >>>>>> On 10/3/17 10:10 AM, stdp82(a)virgilio.it wrote: >>>>>>> Many thank for your response. >>>>>>> Claryfing my question on point 3, >>>>>>> When I look in group.effect.slope, the map show the group difference >>>>> removing >>>>>>> the effect of the covariate. >>>>>>> Conversely, I would to obtain the map reporting only the effect of >>>>> covariate >>>>>>> on dependent variable (functional connectivity). >>>>>>> Is possible to look on it? >>>>>>> Regards >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> Data: 2-ott-2017 16.58 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/01/2017 05:08 PM, stdp82(a)virgilio.it wrote: >>>>>>>>> Hi, >>>>>>>>> on 4 groups, 1 covariate (4GV1) >>>>>>>>> >>>>>>>>> I run mri_glmfit using the following .mtx >>>>>>>>> >>>>>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>>>>>>> should be >>>>>>>> >>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>> >>>>>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>>>>> C15) group.effect.intercept >>>>>>>>> 1 -1 0 0 0 0 0 0 >>>>>>>>> 1 0 -1 0 0 0 0 0 >>>>>>>>> 1 0 0 -1 0 0 0 0 >>>>>>>>> C16) group.effect.slope >>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>> >>>>>>>>> Please: >>>>>>>>> 1) Could you check whether the all .mtx are complete and corrected, in >>>>>>>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs- gr3+gr4. >>>>>>> slope? >>>>>>>> they look correct, except for the one i noted >>>>>>>>> 2) Could you explain the meaning of: >>>>>>>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 >>> differ >>>>>>> from that of grp3 and 4 >>>>>>>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>>>>>>> group.effect.slope - interaction between group and covariate >>>>>>>>> group.effect.intercept - is there an effect of group on the inercept >>>>>>>>> 3) Which is the contrast identifying the effect of covariate on group >>>>>>>>> differences? >>>>>>>> not sure what you mean >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Best regards >>>>>>>>> >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> ----Messaggio originale---- >>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> Data: 5-set-2017 22.59 >>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>>>>>>> >>>>>>>>>> you would need to create a contrast to look for the interaction. If >>> you >>>>>>>>>> have four gruops and 1 covariate, then it would be >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> e.g., by considering two or more groups, I would like to map the >>>>> clusters >>>>>>>>>>> reporting the covariance between the functional connectivity or >>>>> cortical >>>>>>>>>>> thickness (dependent variable) and age, tacking in account the group >>>>>>>>>>> differences. >>>>>>>>>>> Instead, I'm not interested to map the group differences, taking in >>>>>>> account >>>>>>>>>>> the nuisance factors. >>>>>>>>>>> Thanks, >>>>>>>>>>> Stefano >>>>>>>>>>> >>>>>>>>>>>> ----Messaggio originale---- >>>>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>>>>>>> >>>>>>>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>>>> Hi list, >>>>>>>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the >>> dependence >>>>>>>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>>>>>>> Anyway, where I should look if I want assess the the map showing >>> the >>>>>>>>>>>>> clusters in which the dependent variable is associated to >>> covariate, >>>>>>>>>>>>> tacking in account the group difference? Please could you suggest >>> my >>>>>>>>>>>>> the path? >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> Stefano >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>> -- >>>>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>>>> MGH-NMR Center >>>>>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>>>> >>>>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>>>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>> https://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 >>>>>>>>>>> at >>>>>>>>>>>> http://www.partners.org/complianceline . 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 mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>> >>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 12 Oct '17

12 Oct '17

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B- Clusters in which the fMRI (dependent variable) is associated to the structural data (covariate), taking in account the groups (I suppose that the maps will be in the slope folder) ---> MANOVA between 4 groups Please could you check the contrast reported below? I suspect that there are some errors because, looking at results: 1- The slope map is the inverse in color of the intercept map. 2- Newly, I would to verify whether the fcMRI difference observed between groups are associated to change in covariate (volume). C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25 C15) group.effect.intercept 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 C16) group.effect.slope 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 11-ott-2017 17.28 >A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance > >the rational is to make them sum to 1.0 so that the gamma.mgh file has >units of mm (or whatever the input units are). It is unimportant for >p-values. > > >On 10/10/2017 01:54 PM, stdp82(a)virgilio.it wrote: >> Thanks >> >> In which contrast I must change "1" with "0.25"? >> What is the rationale to use 0.25? >> >> >> Sent from Virgilio Mobile >> ________________________________ >> >> Il 10/10/2017, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> ha scritto: >> >> I don't understand what you mean by "where I should use" >> >> I thought I looked through all those contrasts a few weeks ago, no? >> >> >> On 10/10/2017 04:22 AM, stdp82(a)virgilio.it wrote: >>> You have suggested to use >>> 0 0 0 0 .25 .25 .25 .25 >>> to look the map where, considering the group differences, the covariate >>> predicts the dependent variable (functional connectivity) in 4GV1. >>> >>> Below I'm reporting the contrast that I have used. >>> Please could you check it and suggest correction? >>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please? >>> >>> Thanks >>> >>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>> C15) group.effect.intercept >>> 1 -1 0 0 0 0 0 0 >>> 1 0 -1 0 0 0 0 0 >>> 1 0 0 -1 0 0 0 0 >>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>> >>> >>> >>> >>> >>> >>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>> Thank you very much. >>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>> Which are the contrast reported below that I should modify? >>>> >>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>> C15) group.effect.intercept >>>> 1 -1 0 0 0 0 0 0 >>>> 1 0 -1 0 0 0 0 0 >>>> 1 0 0 -1 0 0 0 0 >>>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>>> ----Messaggio originale---- >>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>> Data: 9-ott-2017 22.56 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance >>>> >>>> I don't know what you are asking >>>> >>>> >>>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>>> Thank you very much. >>>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>>> Which are the contrast reported below that I should modify? >>>>> >>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>> C15) group.effect.intercept >>>>> 1 -1 0 0 0 0 0 0 >>>>> 1 0 -1 0 0 0 0 0 >>>>> 1 0 0 -1 0 0 0 0 >>>>> C16) group.effect.slope >>>>> 0 0 0 0 1 -1 0 0 >>>>> 0 0 0 0 1 0 -1 0 >>>>> 0 0 0 0 1 0 0 -1 >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> Data: 3-ott-2017 16.19 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance >>>>>> >>>>>> probably you want 0 0 0 0 .25 .25 .25 .25 >>>>>> >>>>>> >>>>>> >>>>>> On 10/3/17 10:10 AM, stdp82(a)virgilio.it wrote: >>>>>>> Many thank for your response. >>>>>>> Claryfing my question on point 3, >>>>>>> When I look in group.effect.slope, the map show the group difference >>>>> removing >>>>>>> the effect of the covariate. >>>>>>> Conversely, I would to obtain the map reporting only the effect of >>>>> covariate >>>>>>> on dependent variable (functional connectivity). >>>>>>> Is possible to look on it? >>>>>>> Regards >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> Data: 2-ott-2017 16.58 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/01/2017 05:08 PM, stdp82(a)virgilio.it wrote: >>>>>>>>> Hi, >>>>>>>>> on 4 groups, 1 covariate (4GV1) >>>>>>>>> >>>>>>>>> I run mri_glmfit using the following .mtx >>>>>>>>> >>>>>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>>>>>>> should be >>>>>>>> >>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>> >>>>>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>>>>> C15) group.effect.intercept >>>>>>>>> 1 -1 0 0 0 0 0 0 >>>>>>>>> 1 0 -1 0 0 0 0 0 >>>>>>>>> 1 0 0 -1 0 0 0 0 >>>>>>>>> C16) group.effect.slope >>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>> >>>>>>>>> Please: >>>>>>>>> 1) Could you check whether the all .mtx are complete and corrected, in >>>>>>>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs- gr3+gr4. >>>>>>> slope? >>>>>>>> they look correct, except for the one i noted >>>>>>>>> 2) Could you explain the meaning of: >>>>>>>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 >>> differ >>>>>>> from that of grp3 and 4 >>>>>>>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>>>>>>> group.effect.slope - interaction between group and covariate >>>>>>>>> group.effect.intercept - is there an effect of group on the inercept >>>>>>>>> 3) Which is the contrast identifying the effect of covariate on group >>>>>>>>> differences? >>>>>>>> not sure what you mean >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Best regards >>>>>>>>> >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> ----Messaggio originale---- >>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> Data: 5-set-2017 22.59 >>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>>>>>>> >>>>>>>>>> you would need to create a contrast to look for the interaction. If >>> you >>>>>>>>>> have four gruops and 1 covariate, then it would be >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> e.g., by considering two or more groups, I would like to map the >>>>> clusters >>>>>>>>>>> reporting the covariance between the functional connectivity or >>>>> cortical >>>>>>>>>>> thickness (dependent variable) and age, tacking in account the group >>>>>>>>>>> differences. >>>>>>>>>>> Instead, I'm not interested to map the group differences, taking in >>>>>>> account >>>>>>>>>>> the nuisance factors. >>>>>>>>>>> Thanks, >>>>>>>>>>> Stefano >>>>>>>>>>> >>>>>>>>>>>> ----Messaggio originale---- >>>>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>>>>>>> >>>>>>>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>>>> Hi list, >>>>>>>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the >>> dependence >>>>>>>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>>>>>>> Anyway, where I should look if I want assess the the map showing >>> the >>>>>>>>>>>>> clusters in which the dependent variable is associated to >>> covariate, >>>>>>>>>>>>> tacking in account the group difference? Please could you suggest >>> my >>>>>>>>>>>>> the path? >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> Stefano >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>> -- >>>>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>>>> MGH-NMR Center >>>>>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>>>> >>>>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>>>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>> https://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 >>>>>>>>>>> at >>>>>>>>>>>> http://www.partners.org/complianceline . 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 mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>> >>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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volume vs surface-based and surface smoothing
by Alissa Stafford 12 Oct '17

12 Oct '17

Hello, I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess. Registration has 2 parts: 1: the native anatomical space is registered with the fsaverage space. This is happening during recon-all. 2: native functional data is registered with the native anatomical data. This is happening during register-sess in preprocess-sess. Aren’t these both volume-based registrations? If not when are the surfaces created? My concern is that it is volume-based and I was under the impression from this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all registrations should be done on the surface. I am also confused about rawfunc2surf-sess. I believe up until this function in preprocess-sess, everything has been done in the volume so this is the first step that is done in the surface, is that correct? And then does this do smoothing? I realized it has a fwhm input option so it must smooth. So is this where the functional data is now expressed in the surface and it also smooths? Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess? I basically just want to be making sure I understand when registration is volume-based or surface-based and when it’s appropriate to use volume-based. And I was using the rawfunc2surf function assuming it was for smoothing, but I am not so sure if this only creates the surface or also smooths. Thanks, Alissa

1 0

Postdoc position studying MRI measures following vision loss
by Visscher, Kristina M 12 Oct '17

12 Oct '17

A postdoctoral scholar position is available to work on a project using functional and structural MRI to assess how connectivity of visual areas is altered following loss of central vision and increased use of peripheral vision in the Visscher lab at the University of Alabama at Birmingham (https://labs.uab.edu/visscher/) This project is part of the NIH-funded Human Connectome Project, Connectomes in Human Diseases program. Applicants must be motivated and have prior experience with programming and imaging data analysis. Prior work in computational methods, vision, psychophysics, and/or eye tracking is a plus. Please send cover letter detailing your interests and fit with the lab, CV, and contact information for 3 references by email to Kristina Visscher kmv(a)uab.edu<mailto:kmv@uab.edu>. UAB consistently ranks as one of the top locations among US universities for training postdoctoral scholars. Located in Birmingham, Alabama, a metro area of over a million people, where access to technical resources and a collaborative, supportive environment combine to make a strong environment for postdoctoral work, and a very reasonable cost of living makes life on a postdoc salary comfortable. You will have resources and collaborative opportunities from our Civitan International Neuroimaging Lab including our 3T Siemens Prisma scanner, the UAB Center for Low Vision Rehabilitation, the Comprehensive Neuroscience Center, the Alabama Advanced Imaging Consortium, and Auburn University's 7T MRI machine, among other resources. More information about these resources are at https://labs.uab.edu/visscher/resources. Kristina Visscher, Ph.D UAB Neurobiology Department kmv(a)uab.edu<mailto:kmv@uab.edu> | https://labs.uab.edu/visscher/

1 0

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Freesurfer October 2017