Than you so much for your help.
Here are the *.e* files from the First logs directory. I actually don't even see the *_origsegs.nii.gz file. Just the original T1 image, *.bvars,*.vtk, *com, *std_sub.mat, *std_sub.nii.gz, and logs directory. That's it.
again, many thanks.
aj
--- On Fri, 1/29/10, Mark Jenkinson <[log in to unmask]> wrote:
> From: Mark Jenkinson <[log in to unmask]>
> Subject: Re: [FSL] problem with FIRST
> To: [log in to unmask]
> Date: Friday, January 29, 2010, 2:09 AM
> 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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