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> 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