External Email - Use Caution I have a group of stroke patients. Most of them have a left-sided stroke, the others right-sided. I would like to swap the affected right hemisphere with the unaffected left hemisphere in the patients with a right-sided stroke. I have done that successfully following the instructions with xhemi, but is there a way to achieve that for a regular group analysis (e. g. using fsaverage as the target and not to fsaverage_sym).
On Tue, Nov 5, 2019 at 9:24 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > what do you mean "flip" them? > > On 11/5/2019 6:10 AM, Jose Graterol wrote: > > 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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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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