Hi,
The recommended way of getting the volume is to use fslstats on the
*_firstseg.nii.gz volume, as described in:
http://www.fmrib.ox.ac.uk/fsl/first/index.html
If you do not get this output image then that is a serious problem
and needs to be fixed before trying anything else.
Can you please look at the *.e* files in your log directory and
send us the contents (giving the name of the file it comes from)
so that we can try and diagnose your problem?
One thing we have found before is that for images with a limited
FOV, the brainstem and/or cerebellum segmentation can cause
problems. If this is the case you should be able to see it in the
individual segmentation outputs (the *_origsegs.nii.gz file).
Have you checked this file? Do the segmentations all look correct?
And have you checked that the registrations have all worked?
Let us know the answers to the above questions.
All the best,
Mark
On 29 Jan 2010, at 07:24, Adil Javed wrote:
> Hi,
> I am running the script run_first_all on my T1 images. This script
> does not always generates the all_fast_firstseg.nii.gz file, which I
> need to do the volumetric analysis of subcortical structures. It
> does generate all the other .vtk, bvars, and .com files.
> Ant ideas why this happens?
>
> Also, can I use the .vtk file to get the volume info?
> for example: first_utils --meshToVol -m mesh.vtk -i t1_image.nii.gz -
> l fill_value -o output_name
>
> and then get the volume by:
> fslstats output_name -l 16.5 -u 17.5 -V ?
>
> I tried volume analysis using both .vtk and all_fast_firstseg.nii.gz
> files on one of the subjects, but these two methods five different
> results. not sure why this ocurs?
>
> Any ideas?
>
> Tx so much for your help,
>
> aj
>
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