Hi Cheng Wei:

I pre-processed the Burner pipeline, so I will answer your questions for Cameron.

Ans for Q1: You will need to find the labels from the *_phenotypic.csv provided by the competition organizer. There was no information about patients or controls in the original file structure anyway. I used the scanID as the file name, so it is fairly easy to retrieve the information from the datasheet.

Ans for Q2: 
I have not upladed the group average to the NITRC FTP, but in the mean time you can also download from 
http://fmrif.nimh.nih.gov/~chuc2/pub/ADH...
The file name is Template_6.nii
One way to extract brain structrual information is to use an atlas. I often use LPBA40 by LONI. http://www.loni.ucla.edu/~shattuck/resou...
You can affine reigster the Maximum likelibood label map (in the maxprob directory) to the "Template_6.nii". I often use "spm_affreg.m" to do the affine registration, it is part of the SPM package.
The code is here

tmp='/DirectoryOfTheTemplate/Template_6.nii';

src='/DirectoryOfTheLPBA40Label/lpba40.spm5.avg152T1.label.nii

 

vg=spm_vol(tmp);

vf=spm_vol(src);

flags.regtype='none';

[M,scal] = spm_affreg(vg,vf,flags);

N=nifti(src);

N.mat=M*N.mat;

create(N);

 

After affine register the Atlas to the template, choose Coregister(Reslice) in SPM to reslice the atlas. Remember to select "Nearest Neighbour" as the interpolation method.

Now, you can use your resliced atlas as the mask to select brain regions.

 

Best,

Carlton