Hi Doug, Our hypothesis is that cortical thickness will be lower in patients than in volunteers, once controlled for gender, age, education, etc. I may remove MMSE as diagnosis of the patient is in part based on the MMSE scores. In that case, I would have 12 regressors, in the order you listed minus the MMSE-slope ones. Should I be using [0 0 -1 1 0 0 0 0 0 0 0 0] or [0 0 1 -1 0 0 0 0 0 0 0 0] to test my hypothesis?
Cheers, Linda On 7 December 2011 00:01, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > In this case you have 4 class variables and 3 continuous, so you'll have > 16 regressors (and so 16 elements in your contrast). Your actual contrast > vector depends on the order of your class variables in the fsgd. Assuming > that the order is MP, FP, MV, FV, then the regressors will have the > following meaning: > 1. MP-Offset > 2. FP-Offset > 3. MV-Offset > 4. FV-Offset > 5-8. Age-Slope > 9-12. MMSE-Slope > 13-16. Ed-Slope > > The contrast you list below would then compute the average thickness of > the volunteers, probably not what you want. But I'm not sure what contrast > you actually want (not clear from "see if they affect thickness). Can you > be more specific/precise? > doug > > > Linda Zhang wrote: > >> Hi Doug, >> >> Sure, my fsgd file contained two groups originally, M and F. I had three >> continuous variables, which were Age, MMSE, Education. I wanted to test >> whether thickness is correlated with MMSE scores after controlling for >> gender, age and education. I now want to add two more class variables >> (patient and volunteer), and see if they affect thickness. My question was >> asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 >> 0 0]? >> I tried mris_preproc again with a different group, and that worked fine, >> so maybe it was just a fluke. Thanks! >> >> Cheers, >> Linda >> >> >> >> On 5 December 2011 23:10, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> wrote: >> >> >> >> Linda Zhang wrote: >> >> Hi Doug, >> >> Thanks for the clarification. If I were to add another two >> class variables (patient and subject, for example) and I >> wanted to see if they affected thickness, assuming they come >> after gender in the fsgd file, would the contrasts then be [0 >> 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? >> Sorry, I can't remember what your design is (I answer a lot of >> emails and they often blend together). Can you refresh my memory? >> >> >> From the powerpoint slides, there's an example where two >> contrast matrices are used (age, gender), what kind of output >> would that produce? >> >> It would produce results (p-values, eg) for each of the contrasts. >> This allows you to run one command instead of one for each contrast. >> >> >> /home/virtualuser/freesurfer/**subjects/lh.MMSE-AD.thickness.** >> 00.mgh >> doesn't exist, I'm not sure why... >> >> Your mris_preproc failed or you are not in the directory that has >> this file. >> doug >> >> >> Cheers, >> Linda >> >> >> >> >> On 3 December 2011 01:26, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> does >> /home/virtualuser/freesurfer/** >> subjects/lh.MMSE-AD.thickness.**00.mgh >> exist? >> doug >> >> Linda Zhang wrote: >> >> Dear all, >> >> I think I figured out the contrasts (I'm using [0 0 0 0 0.5 >> 0.5 0 0]...is that correct?) but I've come across an error >> when trying to do the next step in the tutorial. >> >> I didn't cache the data during recon-all, so I ran the >> following: >> >> mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage >> --hemi lh >> --meas thickness --out lh.MMSE-AD.thickness.00.mgh >> >> It seemed to run smoothly (I've attached the log below) >> so I >> ran the next step: >> >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval >> lh.MMSE-AD.thickness.10.mgh >> >> I got the following error: >> >> Reading source surface reg >> /home/virtualuser/freesurfer/** >> subjects/fsaverage/surf/lh.**sphere.reg >> Loading source data >> mghRead(/home/virtualuser/** >> freesurfer/subjects/lh.MMSE-**AD.thickness.00.mgh, >> -1): could not open file >> ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 >> >> Can anyone tell me where the problem is? Thanks! >> >> Cheers, >> Linda >> >> The log for mris_preproc (truncated to the last subject and >> last line): >> >> ------------------------------**--------------------- >> #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 >> -------------- >> ----------------------- >> mri_surf2surf --srcsubject avo1249 --srchemi lh >> --srcsurfreg >> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg >> sphere.reg --tval ./tmp.mris_preproc.18275/**avo1249.12.mgh >> --sval >> /home/virtualuser/freesurfer/** >> subjects/avo1249/surf/lh.**thickness >> --sfmt curv --noreshape --no-cortex >> Source registration surface changed to sphere.reg >> Target registration surface changed to sphere.reg >> srcsubject = avo1249 >> srcval = >> /home/virtualuser/freesurfer/** >> subjects/avo1249/surf/lh.**thickness >> srctype = curv >> trgsubject = fsaverage >> trgval = ./tmp.mris_preproc.18275/**avo1249.12.mgh >> trgtype = >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = (null) >> label-trg = (null) >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /home/virtualuser/freesurfer/** >> subjects/avo1249/surf/lh.**sphere.reg >> Loading source data >> Reading curvature file >> /home/virtualuser/freesurfer/** >> subjects/avo1249/surf/lh.**thickness >> Reading target surface reg >> /home/virtualuser/freesurfer/** >> subjects/fsaverage/surf/lh.**sphere.reg >> Done >> Mapping Source Volume onto Source Subject Surface >> surf2surf_nnfr: building source hash (res=16). >> Surf2Surf: Forward Loop (163842) >> >> surf2surf_nnfr: building target hash (res=16). >> Surf2Surf: Reverse Loop (121128) >> Reverse Loop had 15750 hits >> Surf2Surf: Dividing by number of hits (163842) >> INFO: nSrcLost = 0 >> nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = >> 2.2506 >> nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, >> MnSrcMultiHits = 2.36099 >> Saving target data >> Saving to ./tmp.mris_preproc.18275/**avo1249.12.mgh >> >> >> >> ----------------------- >> mri_concat ./tmp.mris_preproc.18275/**avo0015.1.mgh >> ./tmp.mris_preproc.18275/**avo0260.2.mgh >> ./tmp.mris_preproc.18275/**avo0403.3.mgh >> ./tmp.mris_preproc.18275/**avo0441.4.mgh >> ./tmp.mris_preproc.18275/**avo0493.5.mgh >> ./tmp.mris_preproc.18275/**avo0622.6.mgh >> ./tmp.mris_preproc.18275/**avo0677.7.mgh >> ./tmp.mris_preproc.18275/**avo0920.8.mgh >> ./tmp.mris_preproc.18275/**avo1086.9.mgh >> ./tmp.mris_preproc.18275/**avo1206.10.mgh >> ./tmp.mris_preproc.18275/**avo1241.11.mgh >> ./tmp.mris_preproc.18275/**avo1249.12.mgh --o >> lh.MMSE-AD.thickness.00.mgh >> >> >> >> On 2 December 2011 11:42, Linda Zhang >> <lzhan...@gmail.com <mailto:lzhan...@gmail.com> >> <mailto:lzhan...@gmail.com <mailto:lzhan...@gmail.com>> >> <mailto:lzhan...@gmail.com <mailto:lzhan...@gmail.com> >> >> <mailto:lzhan...@gmail.com >> <mailto:lzhan...@gmail.com>>>> wrote: >> >> Dear all, >> >> I have a bit of an amateur question. I've read the >> slides and >> tutorial for group analysis, but I'm still confused >> about the >> contrasts. I made my fsgd file, which contains two >> groups: >> M and >> F. I also have three continuous variables: Age, MMSE, >> Education. I would like to test whether thickness is >> correlated with MMSE >> scores, after controlling for gender, age, and >> education. What >> should my contrast file be in this case? >> Thanks for the help! >> >> Cheers, >> Linda >> >> >> ------------------------------** >> ------------------------------**------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/ >> **freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> >> >> >> 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 Partners >> Compliance HelpLine at >> >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was >> sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
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