Re: [Freesurfer] Accounting for family relation in FS
Yea, the real hard part is figuring out how to model the twins that are split between groups. You might be able to create a bunch of groups. If you've already created a design in FSL that you like, you can extract the design matrix and use it in mri_glmfit with the --X option. Not sure about correcting for multiple comparisons though On 3/8/19 3:13 AM, Julian Macoveanu wrote: External Email - Use Caution Thank you for the reply. The original idea was to have an ANOVA with a group factor “diagnosis” with three levels. We could use an F-test to check for an effect of diagnosis and then perform 3 pairwise group tests (LR vs HR, LR vs ILL, HR vs ILL). Would it help to only implement the two-sample group tests? However, the critical issue to account for correlated data remains since about 80% of the subjects have their co-twin in the same group. The idea behind the model that has a variable with 1s for each twin pair is to model out each pair’s mean. I implemented the model I described in the FSL GLM and estimated with FEAT for the functional data of the group. The second option I had was to perform a permutation based estimation as implemented in PALM and restrict the permutations to between pairs and single subjects. Would any of these options work in FS? Maybe clustering the subjects somehow? Julian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Accounting for family relation in FS
Sorry for the delay ... This looks like a fairly complicated design, and I'm not sure how to think about it. What do you actually want to test in the end? BTW, the FSGD file you have there will not work. The variables are for continuous variables (eg, age) and not discrete variables (eg, sex or Pair_no). On 3/7/19 1:54 AM, Julian Macoveanu wrote: > > External Email - Use Caution > > Dear FS List, > > (apologies for reposting under different title) > > I wanted to check if my GLM design for a surface based analysis is > sound. I am new to FS so please don’t skip over details. > > I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin > pairs may be present in the same group (e.g both are in the low-risk) > or between groups (one of them in high-risk one in affected). Not all > twins have their co-twin in the analysis though. > > In order to account for with-pair variance correlation I was wondering > if this FSGD example with 9 subjects might do it or if there might be > better options. > > GroupDescriptorFile 1 > Title … > Class LR > Class HR > Class ILL > Variables age sex TIV Pair_no1 Pair_no2 Pair_no3 > Input subject1 LR 30 M 123456 1 0 0 > Input subject2 LR 30 M 123456 1 0 0 > Input subject3 LR 23 F 123456 0 0 0 > Input subject4 HR 20 F 123456 0 1 0 > Input subject5 HR 21 F 123456 0 0 1 > Input subject6 HR 22 M 123456 0 0 0 > Input subject7 ILL 20 F 123456 0 1 0 > Input subject8 ILL 21 F 123456 0 0 1 > Input subject9 ILL 35 F 123456 0 0 0 > > I do have 60+ pairs so it will be a lot of variables. I know that PALM > has an options to provide an exchangeability file, but FsPalm seems to > perform corrections for multiple comparisons only. > > Julian > > > > > ___ > 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
[Freesurfer] Accounting for family relation in FS
External Email - Use Caution Dear FS List, (apologies for reposting under different title) I wanted to check if my GLM design for a surface based analysis is sound. I am new to FS so please don’t skip over details. I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin pairs may be present in the same group (e.g both are in the low-risk) or between groups (one of them in high-risk one in affected). Not all twins have their co-twin in the analysis though. In order to account for with-pair variance correlation I was wondering if this FSGD example with 9 subjects might do it or if there might be better options. GroupDescriptorFile 1 Title … Class LR Class HR Class ILL Variablesage sex TIV Pair_no1 Pair_no2 Pair_no3 Input subject1 LR 30 M 123456 1 0 0 Input subject2 LR 30 M 123456 1 0 0 Input subject3 LR 23 F 123456 0 0 0 Input subject4 HR 20 F 123456 0 1 0 Input subject5 HR 21 F 123456 0 0 1 Input subject6 HR 22 M 123456 0 0 0 Input subject7 ILL 20 F 123456 0 1 0 Input subject8 ILL 21 F 123456 0 0 1 Input subject9 ILL 35 F 123456 0 0 0 I do have 60+ pairs so it will be a lot of variables. I know that PALM has an options to provide an exchangeability file, but FsPalm seems to perform corrections for multiple comparisons only. Julian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
