Hi,
I am not really sure what you are saying here.
What *exactly* was the error that you found in the log files?
I cannot really help with only an indication that "return error in
open file nifty".
I need more specific information.
As for the output_all_fast_origsegs - it sounds like it produced
a valid mask for the structure (as many of these subcortical
structures are "potato-like"). Did you overlay it on the original
image to see if it had succeeded in finding a valid structure?
I would not be too concerned about your conversion to nifti
at this stage. The methods you mention sound fine. I think it is
more likely to be how you are using the tool and whether there is
something odd (e.g. artefact) inside your images.
If you can give me some more information then I can hopefully help.
All the best,
Mark
On 23 Aug 2009, at 18:10, diagnostico imagenes wrote:
> Hello Group!
> Hi Mark,thanks!
>
>
> I use cat *.e* and return error in open file niifty
>
> and fslview output_all_fast_origsegs.nii.gz generates an object
> similar to a potato
>
> ------------------------------------------------------------------------
> I am working with the FSL-first and
> maybe my mistake is in the creation of the format nii.gz
>
> because run run_first_all generate errors name_archive.logs
> (directory)
>
>
> creation of the format nii.gz
>
> I use
> MRICONVERT dicom->FSL (IMAGE.hdr IMAGE.img)
> http://lcni.uoregon.edu/~jolinda/MRIConvert/
>
> then
> MRICRON
> http://www.sph.sc.edu/comd/rorden/mricron/
> open IMAGE.hdr /img
> and save nii.gz
>
> Is this right?
>
> also use
> fslchfiletype
>
> http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html
>
> (also generates error in run_first_all)
>
>
> thanks , Nicolas.
>
> FSL 4.1.4
>
>
>
> ----------------------------------------------------------------------------------------------------
>
> > Date: Thu, 20 Aug 2009 16:15:39 +0100
> > From: [log in to unmask]
> > Subject: Re: [FSL] First Volumen hippocampus ?
> > To: [log in to unmask]
> >
> > Hi,
> >
> > Sounds like something (maybe one structure) is failing.
> > Can you look in the log directory and see if any of the
> > *.e* files contain an error message? Just doing
> > cat *.e*
> > inside that directory will do the job.
> >
> > Also, look at the file output_all_fast_origsegs.nii.gz in
> > FSLView and see if it is doing a reasonable job.
> >
> > All the best,
> > Mark
> >
> >
> > On 20 Aug 2009, at 16:10, diagnostico imagenes wrote:
> >
> > > Hi group!
> > >
> > > Hi Mark & Tom
> > >
> > > Download and Install 4.1.4 FSL
> > > and RUN
> > >
> > > run_first_all -i con01.nii.gz -o output
> > >
> > > and returns:
> > >
> > > output-L_Accu_first.vtk
> > > output-L_Amyg_first.vtk
> > > output-L_Hip_first.vtk
> > >
> > > .
> > > .
> > > .
> > > output-R_Hip_first.vtk
> > > output_to_std_sub.nii.gz
> > > output_to_std_sub.mat
> > > output.logs -->directory, for example: clean_up.e12523.1 ,
> > > first.e4519.17, first_flirt.o4325, first.o4519.2,
> > > output.com
> > > output_all_fast_origsegs.nii.gz
> > >
> > > But, no return's
> > >
> > > output_all_fastfirstseg_.nii.gz
> > >
> > > thanks, Nicolas.
> > >
> > >
> > > Gratis y optimizado para MSN Nuevo Internet Explorer 8
>
> Gratis y optimizado para MSN Nuevo Internet Explorer 8
|