[Freesurfer] Matlab crash dump when running the segmentation of longitudinal hippocampal subfields
External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze longitudinal hippocampal subfields for many subjects on a server, but when I run the command longHippoSubfieldsT1.sh, for some subjects, I get the error for Matlab and a file called matlab_crash_dump. I've searched the list and no similar request have been submitted. Does anyone have any thoughts on how to solve this problem? Also, Ive attached the matlab_crash_dump file. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 7 3)matlab_crash_dump file: see attached Best regards, Guodong matlab_crash_dump.12390-1 Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] LME model contrast matrix
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? 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? 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? Thanks in advance! Best regards, Guodong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] LME model contrast matrix (Diers, Kersten /DZNE)
> 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 + > From: "Diers, Kersten /DZNE" > Subject: Re: [Freesurfer] LME model contrast matrix > To: "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 > 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<mail
Re: [Freesurfer] LME model contrast matrix (Diers, Kersten /DZNE)
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 + > From: "Diers, Kersten /DZNE" > Subject: Re: [Freesurfer] LME model contrast matrix (Diers, Kersten > /DZNE) > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: <1572947286.4016.34.ca...@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 + >>> From: "Diers, Kersten /DZNE" >>> Subject: Re: [Freesurfer] LME model contrast matrix >>> To: "freesurfer@nmr.mgh.harvard.edu" >> 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.? >>> >>>
