While I am afraid I can offer no specific advice for VBM in FSL, I do have a general piece of advice.

 

When I see a null result I think is suspicious, I immediately drop threshold and take a look. As instead, instead of p < 0.05 corrected, try viewing the t-map without a threshold. . See if there looks like an appropriate level of variability in the t-stats, or if it looks off (zero at many data points, really speckled).

 

This is a way to QC check the output and see if maybe something went wrong which caused the stats to mess up.

 

Good luck

 

Colin Hawco, PhD

Neuranalysis Consulting

Neuroimaging analysis and consultation

www.neuranalysis.com

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,

 

 

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Rosalia Dacosta Aguayo
Sent: May-19-16 4:35 AM
To: [log in to unmask]
Subject: [FSL] No results with VBM

 

Dear FSL experts,

I have been working with 46 MRI images in order to find some correlations between on cognitive function and gray matter structures (deep gray matter structures).

Pre-processing steps were as follow:

1. Cutting long necks

2. Noise correction

3. Bias field correction

4. Skull-stripping (using CAT12, (Tool for SPM12)  because with bet I got that many images were not fine...as I had to decide wether improve this step manually...(methodology is not as strong and homogeneous as one could expect...or using another tool that gives good results..). With this Tool I got excellent results for all the images...and I after doing an homogeneity analysis, I discarded one of them...so n = 45

5. I used the skull stripped images in the first step of FSLVBM (that is: after doing first step, I reemplaced the skull stripped images created by the ones I got from CAT12).

6. Following fslvbm processes were fine, I visually inspect the GM template as well as the 4D_GM template and it was very good. Images were well aligned...

The problem:

I run correlation analysis between my template (with a gaussian kernel of 3 sigma) and my cognitive variable of interest regressing out for TIV, Age and Gender. It seems that my cog variable is not related to any structure...what I think it is not possible and I was thinking about if I missed something in the way or if my design.mat is not fine (I attach you the design files...)....

Thank you a lot for your helping,

Kind regards,

Rosalia