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 β1 and β2 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 > > > > 在 2019年10月25日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道： > > > > Send Freesurfer mailing list submissions to > > freesurfer@nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-requ...@nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-ow...@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. time point exlusion file exceed nframes (Lauri Tuominen) > > 2. Re: time point exlusion file exceed nframes > > (Greve, Douglas N.,Ph.D.) > > 3. Re: Learning fsfast tutorial (Greve, Douglas N.,Ph.D.) > > 4. Re: LME model contrast matrix (Diers, Kersten /DZNE) > > 5. Re: Learning fsfast tutorial (Renew Andrade) > > 6. Re: Learning dti processing tutorial (Renew Andrade) > > 7. mri_cvs_register error while diffusion imaging processi > > ng > > (Renew Andrade) > > > > > > ----------------------------------------------------------------- > > ----- > > > > Message: 1 > > Date: Wed, 23 Oct 2019 17:34:59 +0000 > > From: Lauri Tuominen <ljt...@utu.fi> > > Subject: [Freesurfer] time point exlusion file exceed nframes > > To: "freesurfer@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.ed > > u> > > Message-ID: <6506f69c-782a-4074-a898-17e58814e...@utu.fi> > > Content-Type: text/plain; charset="utf-8" > > > > External Email - Use Caution > > > > Dear Freesurfers, > > I am running resting state analysis. I have TR 2.3, and 209 time > > points/frames, total length of the scan 483 seconds. I don?t drop > > any frames from the beginning ( nskip = 0 ). > > > > For one subject, the last two time points are motion outliers. So > > my tpef file includes numbers 478.4 and 480.7. When I run selxavg3- > > sess, I get the error time point exlusion file exceed nframes. > > > > I can?t figure out where the bug might be. So once again I would > > really appreciate your help! > > Thanks > > Lauri Tuominen > > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 24 Oct 2019 03:28:21 +0000 > > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > > Subject: Re: [Freesurfer] time point exlusion file exceed nframes > > To: "freesurfer@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.ed > > u> > > Message-ID: <fee25413-e204-29d7-27c0-a69427052...@mgh.harvard.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Lauri, I think this comes down to whether you start counting > > from 0 > > or 1. FSFAST starts from 0, so the time of? time point N is N*TR. > > The > > maximum you can have is N=208, and so the max time would be 478.4. > > Your > > 480.7 exceeds this limit. > > doug > > > > On 10/23/2019 1:34 PM, Lauri Tuominen wrote: > > > > > > External Email - Use Caution > > > > > > Dear Freesurfers, > > > I am running resting state analysis. I have TR 2.3, and 209 time > > > points/frames, total length of the scan 483 seconds. I don?t drop > > > any frames from the beginning ( nskip = 0 ). > > > > > > For one subject, the last two time points are motion outliers. So > > > my tpef file includes numbers 478.4 and 480.7. When I run > > > selxavg3-sess, I get the error time point exlusion file exceed > > > nframes. > > > > > > I can?t figure out where the bug might be. So once again I would > > > really appreciate your help! > > > Thanks > > > Lauri Tuominen > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 24 Oct 2019 03:29:14 +0000 > > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > > Subject: Re: [Freesurfer] Learning fsfast tutorial > > To: "freesurfer@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.ed > > u> > > Message-ID: <a582080c-85f2-9a05-6dad-d4cfba600...@mgh.harvard.edu> > > Content-Type: text/plain; charset="windows-1252" > > > > look in sess01/bold, you should see 001 and 002. Do you? > > > > On 10/22/2019 9:40 AM, Renew Andrade wrote: > > > > External Email - Use Caution > > > > Dear experts: > > I am trying to run preproc-sess -s sess01 -fsd bold -stc up > > -surface fsaverage lhrh -mni305 -fwhm 5 -per-run > > But the outcome is ERROR: no run directories found. > > > > What could be wrong? > > If you need more information let me know! > > > > Sincerely, > > Andrade. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:freesur...@nmr.mgh.harvard.ed > > u> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachmen > > ts/20191024/4f742281/attachment-0001.html > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 24 Oct 2019 08:06:28 +0000 > > From: "Diers, Kersten /DZNE" <kersten.di...@dzne.de> > > Subject: Re: [Freesurfer] LME model contrast matrix > > To: "freesurfer@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.ed > > u> > > Message-ID: <1571904388.10840.18.ca...@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@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ------------------------------ > > > > Message: 5 > > Date: Thu, 24 Oct 2019 15:43:37 +0200 > > From: Renew Andrade <andradere...@yahoo.com> > > Subject: Re: [Freesurfer] Learning fsfast tutorial > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: <9a4b8c42-98ce-4771-83b2-4ca66dfdf...@yahoo.com> > > Content-Type: text/plain; charset="utf-8" > > > > External Email - Use Caution > > > > Dear FreeSurfer experts: > > I am trying to use my own data so I don?t have the same tutorial > > structure. I do keep the folder structure as similar as possible in > > order for FreeSurfer to run but I cannot have different sessions > > for example I just have resting or bold but not both. Is it a > > problem when running this analysis? > > > > > > This is my directory structure > > > > > > ? ~ cd /Users/andraderenew/Downloads/2 > > ? 2 git:(master) ? ls > > rest > > ? 2 git:(master) ? cd rest > > ? rest git:(master) ? ls > > dti_FA.nii.gz dti_L2.nii.gz dti_MD.nii.gz dti_S0.nii.gz > > dti_V2.nii.gz > > dti_L1.nii.gz dti_L3.nii.gz dti_MO.nii.gz dti_V1.nii.gz > > dti_V3.nii.gz > > ? rest git:(master) ? > > > > Sincerely, > > Andrade. > > > > > > look in sess01/bold, you should see 001 and 002. Do you? > > > > On 10/22/2019 9:40 AM, Renew Andrade wrote: > > External Email - Use Caution > > > > Dear experts: > > I am trying to run preproc-sess -s sess01 -fsd bold -stc up > > -surface fsaverage > > lhrh -mni305 -fwhm 5 -per-run > > But the outcome is ERROR: no run directories found. > > > > What could be wrong? > > If you need more information let me know! > > > > Sincerely, > > Andrade. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:freesur...@nmr.mgh.harvard.ed > > u <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachmen > > ts/20191024/17361494/attachment-0001.html > > > > ------------------------------ > > > > Message: 6 > > Date: Thu, 24 Oct 2019 15:53:28 +0200 > > From: Renew Andrade <andradere...@yahoo.com> > > Subject: Re: [Freesurfer] Learning dti processing tutorial > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: <752249c9-9336-48e8-9c46-fc0f5dcba...@yahoo.com> > > Content-Type: text/plain; charset="utf-8" > > > > External Email - Use Caution > > > > In other words I cannot process TRACULA without the T1w images of > > my subjects? Because this Parkinson database is from NITRC and I > > only have the diffusion images not the T1. I can practice on other > > subjects that I have both the T1 and diffusion images but I was > > expecting on using this Parkinson tractography and do the analysis. > > In case you want to know is this https://www.nitrc.org/projects/par > > ktdi/ <https://www.nitrc.org/projects/parktdi/>. > > Sincerely, > > Andrade. > > > > Hi, you need to run recon-all on the T1, not on the diffusion scan. > > This will > > produce an anatomical segmentation of each subject based on the > > T1s, which > > TRACULA will then use to extract anatomical priors on white matter > > tracts, to > > aid tractography. When you run trac-all to do the actual > > tractography, then you > > run it on the diffusion scan. > > ________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Renew > > Andrade > > <andradere...@yahoo.com> > > Sent: Friday, October 18, 2019 5:02:35 PM > > To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Learning dti processing tutorial > > > > External Email - Use Caution > > > > I am using a database of NITRC repository > > https://www.nitrc.org/projects/parktdi/ > > <https://www.nitrc.org/projects/parktdi/> . This images have a > > nifti file for > > 1000s/mm^2 and 2500s/mm^2. I don?t know if it is MPRAGE or not. Can > > you help me? > > > > > > > > What is the input file that you are supplying? Often this happens > > when > > the input it a multi-echo MPRAGE. If so, you can run > > mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz > > then use mprage.mgz as the input to recon-all > > > > On 10/12/2019 4:48 PM, Renew Andrade wrote: > > > > > > External Email - Use Caution > > > > > > Dear freesurfer experts: > > > I am trying to learn dti processing. For using Tracula it appears > > > there is a > > > need for running "recon-all -all -i -s? on every subject before > > > starting to > > > run Tracula. But there seems to be a problem. I have a Parkinson > > > dwi images > > > database and every subject gives me an error of the type > > > ?input(s) cannot > > > have multiple frames!?. I am a little bit stuck on this step. Is > > > it a problem > > > of the file as input? Am I putting the wrong file? Can it be done > > > a recon-all > > > analysis to a dwi image? With trackvis I can obtain the results > > > without any > > > problem. My doubt comes from FreeSurfer only and may be my little > > > knowledge > > > about it. > > > Thanks for your help! > > > Sincerely, > > > Andrade. > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu<mailto:freesur...@nmr.mgh.harvard. > > > edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:freesur...@nmr.mgh.harvard.ed > > u <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachmen > > ts/20191024/189d8994/attachment-0001.html > > > > ------------------------------ > > > > Message: 7 > > Date: Thu, 24 Oct 2019 17:31:17 +0200 > > From: Renew Andrade <andradere...@yahoo.com> > > Subject: [Freesurfer] mri_cvs_register error while diffusion > > imaging > > processing > > To: freesurfer@nmr.mgh.harvard.edu > > Message-ID: <1e231996-9125-4466-a2ad-431d3a714...@yahoo.com> > > Content-Type: text/plain; charset="utf-8" > > > > External Email - Use Caution > > > > Dear FreeSurfer experts: > > I am trying to run Spatial Normalization but I cannot get the morph > > file because I get this error. I don?t know what to do with these > > libraries. Do I need to copy them from where they are in freesurfer > > to somewhere else in the Mac? > > > > sh-3.2# mri_cvs_register --mov IXI_25_Guys_T1 > > Using the CVS template as registration target... > > The outdir: > > /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/cvs > > > > Log file is > > /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/cvs/IXI_ > > 25_Guys_T1_to_cvs_avg35.mri_cvs_register.1910241722.log > > > > Thu Oct 24 17:22:55 CEST 2019 > > --mov IXI_25_Guys_T1 > > $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ > > Renes-Air.home > > Darwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep > > 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64 > > asegfname aseg > > Using m3z type morph files. > > dyld: lazy symbol binding failed: Symbol not found: > > ___emutls_get_address > > Referenced from: > > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > > dyld: Symbol not found: ___emutls_get_address > > Referenced from: > > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > > Abort > > > > > > > > > > > > Sincerely, > > Andrade. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachmen > > ts/20191024/75afbb70/attachment-0001.html > > > > ------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > End of Freesurfer Digest, Vol 188, Issue 37 > > ******************************************* > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
