Hi,
If you have run the standard commands for FIRST, as in our wiki, then the registration to the MNI is done in order to be able to move the standard-space model into the native space. So the segmentation and volumes are created in native space, not standard space.
If you run the vertex analysis then one of the options is to use the --useReconMNI option, which then transforms the coordinates into standard space, effectively normalising things. But if you do not do this (either using a different option or not doing vertex analysis) then you would need to do a separate normalisation if you wanted to account for the effects of brain/head size.
I hope this helps.
All the best,
Mark
On 10 Jul 2014, at 01:32, Reema Jayakar <[log in to unmask]> wrote:
> Hello FSL-FIRST experts,
>
> I have used FIRST to obtain hippocampus volumes for a neurological patient group and a neurotypical control group. As part of the typical workflow laid out in the FIRST documentation, the brains were registered to MNI space and registrations visually inspected. After that segmentations were run as per FIRST documentation.
>
> Are the hippocampal volumes yielded by the FIRST script/fslstats uncorrected? Or normalised?
>
> My understanding (from previous listserv postings) is that because my analyses were done on brains registered in MNI space, each subject has been registered to the standard space and this consequently normalises for brain size. Therefore, I would not need to use total brain volume (nor total intracranial volume) as a covariate in my statistical analyses (group comparisons).
>
> Is this correct? Or am I missing something here.
>
> Manuscript reviewers (may not be familiar with FIRST) suggested that I use normalize hippocampus volumes by computing either total brain volume or intracranial vault volume and then statistically entering those data as a covariate in my model.
>
> If my initial line of thinking is correct (i.e., registering to MNI space takes care of normalizing hippocampus volume), is there a good reference/citation that I can provide to reviewers?
>
> Any help will be really appreciated!
> Thank you so much,
> Reema Jayakar
> Clinical Neuropsychology Doctoral Candidate
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