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 <greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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
       <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
       <mailto:greve@nmr.mgh.harvard.edu

       <mailto:greve@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
       <lzhang87@gmail.com <mailto:lzhang87@gmail.com>
              <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>>
       <mailto:lzhang87@gmail.com <mailto:lzhang87@gmail.com>

              <mailto:lzhang87@gmail.com
       <mailto:lzhang87@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


                     ------------------------------------------------------------------------

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   MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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