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