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> 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>> 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>>> 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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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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