Hi,
The number is a job number, which is useful if you are using a cluster
running Sun Grid Engine, but otherwise just ignore it.
To measure the volume you need to find the appropriate number
either by looking up the structure on:
http://www.fmrib.ox.ac.uk/fsl/first/cma_subcortical_label.html
or by finding the value in the *_firstseg.nii.gz file when viewed
with FSLView.
Once you have this number (e.g. 17 = left hippocampus) you
use fslstats to measure the volume. For example:
fslstats study1_all_fast_firstseg.nii.gz -l 16.5 -u 17.5 -V
which gives you the volume in voxels and in mm^3.
Hope this helps.
All the best,
Mark
On 2 Sep 2009, at 03:56, Chien-Han Lai wrote:
> Dear FSL experts:
> I have some questions about FIRST usage.
> (1) When I perform group FIRST (run_first_all), I find that some
> numbers appear in the terminal window during FIRST steps. (one
> number shows after one patient's T1 image is "FIRST" completed) Can
> anybody tell me what the number means? the all subcortical areas
> volume? or what?
> (2) How do I transform individual output file to volume (by what
> kind of command)?
> Any suggestion will be appreciated much.
> Thank you.
> Sincerely yours
> Dr. Lai
>
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