External Email - Use Caution Thanks a lot Martin for the information. We have actually 2 sessions of placebo for each subject. How do you suggest to do the analysis including that data? BR
On Mon, 30 Jan 2023 at 16:30, Reuter, Martin,Ph.D. <mreu...@mgh.harvard.edu> wrote: > Hi Amirhossein, > > - If you have two time points for all participants, > - and the time difference is the same for all > you can simply subtract the thickness (or volume) values per participant > and run a regular GLM. LME is a little overkill here. > > > In LME, you have one column of ones, and one of the time (which is 0 and t > alternating ) , this is not the time difference! The first time point is > at time 0 and the second at time t (in hours or days whatever). If the time > really does not matter, you can also put 0 and 1. > > You can run the model with no random effect or with one random effect. The > wiki > https://secure-web.cisco.com/1pVifRNw5er1Lzc_ccwFC4C2YEYU4u84Wg9uAV_jJXoNhscogr7v_JipyzF28LHmewwkoWl19W9OH9e9wwz502tCA0t1_FALxC8nFNk1kCoiT1bIZJKvSWv3kYqvbvUJI22kjCf4QZAp-imXgP3CuAMub326jyEz0Yl0OamT5C0gRvQxzroaQmyUmyjfvofQ1Ue9394B6pAprHBE63UK7HveGDF42bam9KA1FKnr0LPRYYW0zwNaYhGJiYr5XBrsHM4Ix-OOicVuCd6em6DD2WAFXONP9dy5ftZxtEQhXuH8uGiDHgTb9ioKlNvSXtnV6vT_gHB_-uy7ZG_85ZO9gzw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels > describes how to compare those models, also how to compute significance. > > You probably have more columns (also if you do the GLM) e.g. the amount of > drug that was given, or who got the drug and who got placebo. Otherwise you > cannot check for a drug effect. That column would be the one you are > interested in. > > Without a placebo group, you will find difference across time, but you > will not know if they are from the drug or from the fact that people are > familiar with the scanner (less head motion) or more annoyed by the scanner > (more head motion) or more tired, or more dehydrated, or rehydrated if you > give the drug with water, or simply a time-of-the-day effect, or scanner > heats up etc. > > Some of these confounders are problematic anyway, as the drug can have a > sedative effect (less motion?) or was given with water (re-hydration). The > second can be controlled by giving placebo with the same amount of water. > Disentangling motion from drug effect (due to the possible correlation) > would only be possible if you separately measure motion or take fMRI or > diffusion motion estimates as a proxy for motion during T1. > > > Head motion reduces grey matter estimates: > doi.org > <https://secure-web.cisco.com/1e_P8iI_a0AjzM6otpiIKFIie8xPaSUrn_hDo3gC-Cw3mJr6_QJ0y4SvUQNF437reTYvJC_yg1IQFS46nslAKbWVTirgEI06ZV-ZULsP6k9WMDhHqV48MTRMyGdotkdNclTL0fBthajVX6Q7ROmtZe79OFT5OVfMJBxSaUdn73A2TcSGg0OY1EX6AivNMR8M00cXY51nOJrrtts779DGVll1dnqJxPnsmvg9tbvGiCGV9fPV0p6JhOUvMz1lZbHMFWB53Dl6cOhIbug2-hVjV9qk1JPuYGQgpVXUH6vPoH8zpnBaRHBBGl4fzxb-LUW8tEnhNksZl3VyWlgBXoHOhlA/https%3A%2F%2Fdoi.org%2F10.1016%2Fj.neuroimage.2014.12.006> > <https://secure-web.cisco.com/1e_P8iI_a0AjzM6otpiIKFIie8xPaSUrn_hDo3gC-Cw3mJr6_QJ0y4SvUQNF437reTYvJC_yg1IQFS46nslAKbWVTirgEI06ZV-ZULsP6k9WMDhHqV48MTRMyGdotkdNclTL0fBthajVX6Q7ROmtZe79OFT5OVfMJBxSaUdn73A2TcSGg0OY1EX6AivNMR8M00cXY51nOJrrtts779DGVll1dnqJxPnsmvg9tbvGiCGV9fPV0p6JhOUvMz1lZbHMFWB53Dl6cOhIbug2-hVjV9qk1JPuYGQgpVXUH6vPoH8zpnBaRHBBGl4fzxb-LUW8tEnhNksZl3VyWlgBXoHOhlA/https%3A%2F%2Fdoi.org%2F10.1016%2Fj.neuroimage.2014.12.006> > <https://secure-web.cisco.com/1e_P8iI_a0AjzM6otpiIKFIie8xPaSUrn_hDo3gC-Cw3mJr6_QJ0y4SvUQNF437reTYvJC_yg1IQFS46nslAKbWVTirgEI06ZV-ZULsP6k9WMDhHqV48MTRMyGdotkdNclTL0fBthajVX6Q7ROmtZe79OFT5OVfMJBxSaUdn73A2TcSGg0OY1EX6AivNMR8M00cXY51nOJrrtts779DGVll1dnqJxPnsmvg9tbvGiCGV9fPV0p6JhOUvMz1lZbHMFWB53Dl6cOhIbug2-hVjV9qk1JPuYGQgpVXUH6vPoH8zpnBaRHBBGl4fzxb-LUW8tEnhNksZl3VyWlgBXoHOhlA/https%3A%2F%2Fdoi.org%2F10.1016%2Fj.neuroimage.2014.12.006> > > Dehydration effects: > [image: 12.cover-source.jpg] > > Responses of the Human Brain to Mild Dehydration and Rehydration Explored > In Vivo by 1H-MR Imaging and Spectroscopy > <http://secure-web.cisco.com/1t9KdLgaaOX0ZM8q84nAgqzxuwxzOE7mU6W8L9Xf2vgU34gxEtyG2Zcx557UOSHgoNdN49Uy--wXidOihtVmF9VBDcwIi6GXK4c-fI6xsd0VLgD1yc30AOeIMNBdY-WvgV-sepvsAql3Tdi9OKH248IzQH0t-cXbj3q_HlbowpgfWh6Zbzw9dGMuZUpftxn6Gp-Ycq8od7JVV4DikAMkhj2y-8JdyHdUSU3JJkETfUVntjuAVBZ5AN_y-1pI39bu3w95rTUrH9BhH2ic1xtlG1hASibJjoDsnj87lYMrp6h4urWndK0g1UHCj-Scz0voeCsI6nuyoAYkEJEZLjFog8g/http%3A%2F%2Fwww.ajnr.org%2Fcontent%2F36%2F12%2F2277.long> > ajnr.org > <http://secure-web.cisco.com/1t9KdLgaaOX0ZM8q84nAgqzxuwxzOE7mU6W8L9Xf2vgU34gxEtyG2Zcx557UOSHgoNdN49Uy--wXidOihtVmF9VBDcwIi6GXK4c-fI6xsd0VLgD1yc30AOeIMNBdY-WvgV-sepvsAql3Tdi9OKH248IzQH0t-cXbj3q_HlbowpgfWh6Zbzw9dGMuZUpftxn6Gp-Ycq8od7JVV4DikAMkhj2y-8JdyHdUSU3JJkETfUVntjuAVBZ5AN_y-1pI39bu3w95rTUrH9BhH2ic1xtlG1hASibJjoDsnj87lYMrp6h4urWndK0g1UHCj-Scz0voeCsI6nuyoAYkEJEZLjFog8g/http%3A%2F%2Fwww.ajnr.org%2Fcontent%2F36%2F12%2F2277.long> > <http://secure-web.cisco.com/1t9KdLgaaOX0ZM8q84nAgqzxuwxzOE7mU6W8L9Xf2vgU34gxEtyG2Zcx557UOSHgoNdN49Uy--wXidOihtVmF9VBDcwIi6GXK4c-fI6xsd0VLgD1yc30AOeIMNBdY-WvgV-sepvsAql3Tdi9OKH248IzQH0t-cXbj3q_HlbowpgfWh6Zbzw9dGMuZUpftxn6Gp-Ycq8od7JVV4DikAMkhj2y-8JdyHdUSU3JJkETfUVntjuAVBZ5AN_y-1pI39bu3w95rTUrH9BhH2ic1xtlG1hASibJjoDsnj87lYMrp6h4urWndK0g1UHCj-Scz0voeCsI6nuyoAYkEJEZLjFog8g/http%3A%2F%2Fwww.ajnr.org%2Fcontent%2F36%2F12%2F2277.long> > > > Best, Martin > > > > On 30. Jan 2023, at 15:18, amirhossein manzouri <a.h.manzo...@gmail.com> > wrote: > > > > Hi, > I have 2 sessions of data acquired in the same day for each participant > before and after the drug intake. I wonder how to analyse this with LME > tool. I create design matrix X in 2 columns, first all ones and second the > time differences(which are the same) and wonder if I need to only run the > model with one random effect like > > lhTh0_1RF = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3); > > And what would be the next steps to get the stats and sig.mgh > > Best regards, > Amirhossein Manzouri > > > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1Soma_Jv2D3v65EVhiRlp3N_lY_u17jLzODtOQXfB7cHB9AoOVsWBj7Sx_fCSSakWrw2FdgBvujP5xEEAFhkoYCg3PuTGXU3E7E6JIZV0SQvNByoAlfytRkTOjXCN00A5cGYp7XhK-7MluC4bGYaDlCEpFgQkZ2M84H_GbNqmYfts9oUL2iW1d8dT4OYDFmoYI9IrWcwPXwa7fPwHWnzKPgrYkAAzp7h41ek8EnvFSKJmpqFkY2DwpLUVsZVbyuzhWEsPejDyVuaGO9dukoWJUyukOTXfkciTHx2IAUvUDXuy9kL0Vnkt9KAPMV99scdcwAktivS7eubS4m8i-LafPg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . > -- Best regards, Amirhossein Manzouri
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