On 8 August 2013 00:40, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

It is hard to say what could be causing the difference. I would look at the uncorrected maps when you get a chance in order to see how different they are.
doug

On 08/07/2013 12:33 PM, Sinead Kelly wrote:

Hi Doug,

I can't visualize the maps on the linux server I'm using but I have the cluster summary files below for DODS and DOSS. As you can see they are quite different. What do you think might be driving the DODS result? I want to look at the difference in surface area between the two genotype groups while regressing out the effects of age and gender. Is this a non result? Thank you for your help!

Sinead

DODS

ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLow CWPHi NVtxs Annot
1 -3.298 36614 541.01 -26.0 -53.1 62.20.77340 0.76580 0.78100 1177 superiorparietal
2 2.918 9004 1642.43 -8.5 9.7 65.20.01020 0.00840 0.01200 2790 superiorfrontal
3 2.626 126211 363.55 -30.3 -65.2 40.50.98580 0.98360 0.98800 817 inferiorparietal
4 2.441 6490 313.02 -30.5 -35.1 58.40.99660 0.99560 0.99760 693 postcentral
5 2.375 107140 1095.56 -10.9 -57.2 44.70.09720 0.09180 0.10260 2308 precuneus
6 2.347 132687 414.79 -38.6 2.1 24.80.95300 0.94920 0.95680 974 precentral
7 2.284 97632 1510.86 -41.4 -50.0 -14.40.01820 0.01580 0.02060 2446 fusiform
8 2.122 111909 365.94 -49.2 -29.5 -3.00.98480 0.98260 0.98700 837 superiortemporal
9 2.070 74111 444.95 -54.7 -42.0 6.30.92120 0.91620 0.92600 998 bankssts
10 1.809 85712 281.07 -57.0 -30.8 21.70.99860 0.99800 0.99920 598 supramarginal
11 1.796 121724 312.87 -10.0 64.3 6.50.99660 0.99560 0.99760 485 superiorfrontal

DOSS
ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
1 -2.520 76782 605.90 -27.7 5.0 51.5 0.66030 0.65420 0.66640 1055 caudalmiddlefrontal
2 2.125 116630 316.10 -36.3 -83.8 -15.4 0.99640 0.99560 0.99720 415 lateraloccipital
3 -2.076 80150 568.86 -40.2 6.5 20.9 0.73090 0.72520 0.73660 1240 parsopercularis

On 5 August 2013 05:05, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

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.

<http://www.researchgate.net/publication/236906359_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

VariablesAge
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_glmfi*t 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 <tel:9004%C2%A0%C2%A0%201642.43> -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 <tel:121724%C2%A0%C2%A0%C2%A0%20312.87> -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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Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8

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Douglas N. Greve, Ph.D.
MGH-NMR Center
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Sinead Kelly

Neuropsychiatric Genetics Group

Trinity Centre

St. James's Hospital

Dublin 8