External Email - Use Caution I believe I found my problem. I was trying to run the analysis with xhemi. Therefore it asked for 34 inputs (17subjects * 2 hemispheres). I was doing it that way because I flipped the hemispheres of the right affected stroke subjects. That was done with fscalc mul -1.
Now I have another question, would it still be possible to flip the hemispheres with fscalc while doing a normal group analysis? Or is there another way to flip them? I want to flip the hemispheres to have all the affected just in one side (e. g. the left hemisphere). Thanks in advance. On Thu, Oct 31, 2019 at 7:10 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > There are not any restrictions, just do the same as you would for a > non-paired analysis. In any event, you are creating a linear model > y = a +b1*x1 + b2*x2 ... > where y is the input (paired diff) and x1, x2, etc, are your factors. > You are the one who knows your data and what models would be appropriate > > On 10/31/19 12:41 PM, Jose Graterol wrote: > > > > External Email - Use Caution > > > > My doubt is, if it is possible to use a FSGD file to add variables to > > a --paired-diff analysis. If it is, what would be the right way to > > format the FSGD file. > > > > Thanks in advance. > > > > On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > I don't understand. What per hemisphere variable? > > > > On 10/25/2019 3:15 AM, Jose Graterol wrote: > >> > >> External Email - Use Caution > >> > >> Thanks for your answer. A follow up question: > >> How should I then specify the variable's values per hemisphere > >> while making the FSGD file if I want to add covariates when > >> running mri_glmfit? > >> > >> Thanks in advance. > >> > >> On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D. > >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > >> > >> If you are trying to determine whether the hemispheres are > >> different, > >> then you need to do the subtraction between the hemis (ie, the > >> --paired-diff). If you want to look at the hemispheres > >> separately, then > >> don't combine them in a single file > >> > >> On 10/21/19 4:58 AM, Jose Graterol wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Thanks for your answer. > >> > > >> > I want to correlate TMS values in 17 stroke patients. > >> Following the > >> > instructions provided to Anders in this link > >> > > >> > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1 > >> > >> > I created the --y file that joins the affected hemispheres > >> together > >> > and the unaffected hemispheres together. I omitted the > >> --paired-diff > >> > flag. When I run mri_glmfit with --fsgd it asks for 34 > >> inputs. I am > >> > guessing those are for the 34 hemispheres of the patients > >> in the order > >> > mentioned in my first email. Would this be the right way to > >> correlate > >> > the variables? > >> > > >> > In short, I am trying to test if there is a difference in > >> cortical > >> > thickness, while adding covariates, between the affected and > >> > unaffected hemispheres in stroke patients. > >> > > >> > Thanks in advance > >> > > >> > On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D. > >> > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > >> <mailto:dgr...@mgh.harvard.edu > >> <mailto:dgr...@mgh.harvard.edu>>> wrote: > >> > > >> > What are you trying to test? Usually you don't have lh > >> and rh in > >> > the same glm > >> > > >> > On 10/17/19 7:09 AM, Jose Graterol wrote: > >> >> > >> >> External Email - Use Caution > >> >> > >> >> Dear Freesurfer Community, > >> >> > >> >> I have a question regarding the formatting of the FSGD > >> file while > >> >> doing an analysis with Xhemi. > >> >> First the --y file was created as previously explained > >> in another > >> >> discussion > >> >> > >> ( > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html > ). > >> >> That is, mris_preproc with --xhemi and no --fsgd flag. > >> >> > >> >> If I understood correctly, that would create a mgh > >> file with the > >> >> following order: sub01lh, sub01rh, sub02lh, sub02rh... > >> >> Then the FSGD file while running mri_glmfit would be: > >> >> GroupDescriptorFile 1 > >> >> Title xxx > >> >> Class sub > >> >> Variables var1 > >> >> Input sub01lh sub var1_lh_sub01 > >> >> Input sub01rh sub var1_rh_sub01 > >> >> Input sub02lh sub var1_lh_sub02 > >> >> Input sub02rh sub var1_rh_sub02 > >> >> > >> >> Would this be correct? If so, what would be the best > >> case for > >> >> specifying a variable like age? Just repeating the > >> value 2 times? > >> >> > >> >> As always, thanks in advance > >> >> > >> >> Kind Regards > >> >> > >> >> José > >> >> > >> >> > >> >> _______________________________________________ > >> >> Freesurfer mailing list > >> >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto: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 > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> <mailto: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 > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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