Hi Sinead, that all looks good. The only thing I would do differently would be to test whether there is a difference in age-area slopes between TT and TG (contrast 0 0 0 0 -.5 -.5 .5 .5). If there is, then that makes the difference of the intercepts between the areas of the groups. If no difference that survives multiple comparisons, then you can re-run your group difference using the DOSS model, ie, add "doss" after the fsgd file on the mri_glmfit command line, and use a contrast of [-.5 -.5 .5 .5 0].  The DOSS model forces the slopes to be the same which assures that the difference in intercept is interpretable.

Finally, if you are using version 5.1 or lower, you will need to get a patch and rerun mris_preproc.

For a description of the method used for correction, you can use the text from Greve, et al,
A Surface-based Analysis of Language Lateralization and Cortical Asymmetry. Journal of Cog Neurosci. 2013.

doug

On 7/30/13 7:53 AM, Sinead Kelly wrote:

Dear freesurfer users,

I would really appreciate if anybody could confirm that I have preformed my analysis correctly as I have very little experience with freesurfer and I want to make sure that my result is a true finding. Firstly, I am looking at the effect of a schizophrenia risk variant on cortical surface area in a large sample of healthy controls.

a. I performed preprocessing on all of my subjects using recon-all.

b. I then qcached my data (resampling it to the average subject - fsaverage) 

c. An FSGD file was then created for statistical analysis to look at differences between TT carriers and TG carriers with age and gender as covariates of no interest. Here is an example of the file I created:

GroupDescriptorFile 1

Title MIR137

Class TTMale

Class TTFemale

Class TGMale

Class TGFemale

Variables Age

Input CON3140 TGFemale 37

Input CON3891 TTFemale 33

Input CON4664 TTFemale 40

Input CON5591 TTMale 41

Input CON7009 TGMale 21

Input CON7024 TTMale 59

Input CON7038 TTMale 56

Input CON7050 TTMale 30

Input CON7054 TTMale 43

Input CON7055 TTMale 43

Input CON7072 TTFemale 41

d. I applied the following contrast:

-0.5 -0.5 0.5 0.5 0 0 0 0 

e. I followed the online tutorial by firstly running the mris_preproc script with area.fwhm10.fsaverage as my input file. Is this correct? (I ran this separately for the left and right hemisphere). 

f. I then ran the mri_glmfit script followed by the mri_glmfit-sim script:

mri_glmfit-sim --glmdir rh.MIR137_area.glmdir --sim mc-z 5000 1.3 mc-z.abs --sim-sign abs --cwpvalthresh .999 --overwrite (I ran this separately for each hemisphere)

Does this look correct?

When this ran I then checked the mc-z.abs.sig.cluster.summary file:

ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ	CWP    CWPLow    CWPHi   NVtxs   Annot
1       -3.298   36614    541.01    -26.0  -53.1   62.2	0.77340  0.76580  0.78100  1177  superiorparietal
2        2.918    9004   1642.43     -8.5    9.7   65.2	0.01020  0.00840  0.01200  2790  superiorfrontal
3        2.626  126211    363.55    -30.3  -65.2   40.5	0.98580  0.98360  0.98800   817  inferiorparietal
4        2.441    6490    313.02    -30.5  -35.1   58.4	0.99660  0.99560  0.99760   693  postcentral
5        2.375  107140   1095.56    -10.9  -57.2   44.7	0.09720  0.09180  0.10260  2308  precuneus
6        2.347  132687    414.79    -38.6    2.1   24.8	0.95300  0.94920  0.95680   974  precentral
7        2.284   97632   1510.86    -41.4  -50.0  -14.4	0.01820  0.01580  0.02060  2446  fusiform
8        2.122  111909    365.94    -49.2  -29.5   -3.0	0.98480  0.98260  0.98700   837  superiortemporal
9        2.070   74111    444.95    -54.7  -42.0    6.3	0.92120  0.91620  0.92600   998  bankssts
10        1.809   85712    281.07    -57.0  -30.8   21.7	0.99860  0.99800  0.99920   598  supramarginal
11        1.796  121724    312.87    -10.0   64.3    6.5	0.99660  0.99560  0.99760   485  superiorfrontal

I have two significant results here - does this look okay? Does this result indicate that surface area of the fusiform and superior frontal significantly differ between  TT and TG carriers (corrected for multiple comparisons?). 

How can I check or report the statistics? Is it possible to extract the values and report descriptive as well as inferential statistics for the result?

I would really appreciate if anyone can validate this for me as I have very little experience with freesurfer.

Thank you for your help!

Sinead

 

Sinead Kelly

Neuropsychiatric Genetics Group

Trinity Centre

St. James's Hospital

Dublin 8

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