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 processing > (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" <freesurfer@nmr.mgh.harvard.edu> > 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" <freesurfer@nmr.mgh.harvard.edu> > 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" <freesurfer@nmr.mgh.harvard.edu> > 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:Freesurfer@nmr.mgh.harvard.edu> > 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/attachments/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" <freesurfer@nmr.mgh.harvard.edu> > 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:Freesurfer@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 > 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/attachments/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/parktdi/ > <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:Freesurfer@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:Freesurfer@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 > 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/attachments/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/attachments/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
