Hi Angela,
> I performed the FIRST analysis using run_first_all via this link: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide, and once completed, I used fslstats to gain volume. I was wondering if the data is normalized when using fslstats.
The volumes are not normalised for head or brain size - have a look at this thread on what you might want to do to correct for this:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;c6c53c1.1510
> Also, I obtained differences between groups in volume but I would like to also have a visual representation of these differences and show that subcortical nuclei are larger in the healthy brain than in the patient brain. Should I use fslmaths to get the average of the images gained from FIRST of each group or should I use fslmerge? I’ve tried fslmerge but get errors involving issues with different dimensions.
To create average images, you would need to register all your segmentations to a common space first. That is an option, but it is probably more straightforward to use FIRST’s tools for vertex analysis. This will allow you to see which parts of each structure change in size. There are detailed instuctions on the FSL wiki on how to go about this.
Hope that helps and let us know if you run into any problems!
Best,
Eelke
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