I have run some volumetric analyses using the first_utils option, so would I be better off going back and using the first_boundary_corr option?
If I were to use the latter option, what is the best method to use (i.e. method as an option in the command below).
first_boundary_corr -s segmented_image -i intensity_image -b method (fast, thresh or none?) -o output_name.
If you use the thresh option, what's the optimal corresponding threshold value?
Thanks,
Liam.
*******************************************
Liam Nestor, Ph.D
Office C8-523
Laboratory for Molecular Neuroimaging
Semel Institute for Neuroscience and Human Behavior
760 Westwood Plaza
Los Angeles 90024
Tel: 310-206-0655
E-mail: [log in to unmask]
*******************************************
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Brian Patenaude [[log in to unmask]]
Sent: Tuesday, June 16, 2009 3:13 PM
To: [log in to unmask]
Subject: Re: [FSL] FIRST .vols file
Hi,
The output in the .vols is the volume in voxels and mm3 (same as output by
fslstats).
Having said that, I do not suggest using that first_utils option anymore
since it will not use the newer boundary correction method that was made
available in the most recent patch (does not require a threshold).
If you send me a couple of pics of the FIRST/manual segmentation and the
first_utils command used to output the .vols file, I'll see if I can spot
anything amiss.
Cheers,
Brian
> Hi,
>
> Could you confirm that the first value in the .vols output file from FIRST
> is the
> number of voxels at a zero percent probablility threshold for spatial
> extent and
> the second is that at 30% threshold? example for left caudate, approx
> 29,000
> and 5000.
>
> Also we're seeing volumes 2 to 3 times larger for the hippocampus using
> FIRST
> relative to those generated by a manual method whereas caudate volumes are
> more similar. Any insight into the possible reasons behind this would be
> appreciated.
>
> Thank you
> Dara
>
>
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