Thanks for the detailed reply Martin. When you say "here we mean really subjects, not time points, as there is only one SPC map per subject", are you referring to the base template name?
Also, as an extension to my previous question, if I have 3 timepoints (tp1, tp2 and tp3). Is it possible for me to compare is pc1 of tp1 vs tp2 is significantly different from pc1 of tp1 vs tp3? If so, would it be a qdec thing or mri_glmfit method? Thanks again Regards Koushik Govindarajan From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Wednesday, July 22, 2015 3:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model Hi Koushik, the output of the long_mris_slopes will be (by default) in each subjects base/template directory, so you would have to map things to, e.g. fsaverage and stack +smooth everythibng before running mri_glmfit. You can also make use of the long_mris_slope flags --stack-spc <out> and --qcache fsaverage to create stacked outputs at different smoothing levels mapped to fsaverage. For running mri_glmfit, you would specify this stacked file as the --y input. That takes care of it (it will use the spc instead of e.g. thickness). The fsgd file needs to have the same order of subjects as in the long.qdec table (here we mean really subjects, not time points, as there is only one SPC map per subject). Generally the FSGD file specifies the order of subjects and other co-variates (e.g. age, IQ, gender). You do not specify the Y (dependent variable) in there. That is only passed on the command line. Best, Martin On 07/22/2015 04:00 PM, Govindarajan, Koushik Athreya wrote: Dear Freesurfers, I am trying to use the longitudinal 2-stage model to run a mri_glmfit analysis. How do I specify my FSGD file so that I compared spc or pc1 maps instead of the regular thickness maps? Also, it is my understanding that I do not have to run mris_preproc and mri_surf2surf since those are part of long_mris_slopes. Is that right? Thanks Koushik Govindarajan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=BQMD-g&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=uGU_kPGWV9zJwznSzn6aV7iTibFh_hK0g0P82rl9ips&s=ohMrnS_1qpz3eFmtAQzXWUFQzl8gYItuIdp1puFN8bc&e=> -- Dr. Martin Reuter Assistant Professor of Radiology Assistant Professor of Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu> reu...@mit.edu<mailto:reu...@mit.edu> Web : http://reuter.mit.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__reuter.mit.edu&d=BQMD-g&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=uGU_kPGWV9zJwznSzn6aV7iTibFh_hK0g0P82rl9ips&s=GCzkNhVEgbCzin7VIZggtYvF1ADNv1xWwRfM9Jr2MOE&e=>
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