Dear Stuart,
This looks correct.
Possibly it is something unusual with your data or some
difference with the manual outlining protocol used by the
CMA to train with versus what you'd prefer to see.
I can't tell without seeing the data, so can you please upload
it to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and send me the reference number.
All the best,
Mark
On 12 Jul 2011, at 17:33, Stuart Currie wrote:
> Hi Mark,
>
> Thanks for replying.
>
> Using first_flirt and after initial registration:
>
> First_flirt input image subject1_to_std_sub_cort
>
>
> I'm trying to calculate cerebellar volume by calculating right and left hemispheres:
>
> e.g. for the left hemisphere:
>
> run_first -i file name -t subject1_to_std_sub.mat -n 33 -o cerebellum -m ${FSLDIR}/data/first/models_336_bin/intref_puta/L_Cereb.bmv -intref ${FSLDIR}/data/first/models_336_bin/05mm/L_Puta_05mm.bmv
>
>
>
> when I view this over the original nii.gz images on fslview it is clear that the cerebellar model is missing some of the peripheral tissue.
>
>
>
> I have tried changing the -n (number of modes of variation) up and down from 33 but 33 seems to be the best fit. Similarly 31 seems to work best for the right hemisphere. Unfortunately when I finally receive the volume data the total cerebellar volumes are ~ 50 cm3, no where near the ~ 110 cm3 expected.
>
>
>
> Is there a way of modifying the cerebellar model further to gain a better fit?
>
>
>
> Cheers
>
>
>
> Stuart
>
>
> On 12 July 2011 16:57, Mark Jenkinson <[log in to unmask]> wrote:
> Can you be a bit more specific?
> All the best,
> Mark
>
> On 12 Jul 2011, at 16:39, Stuart Currie wrote:
>
> > Trying to run the cerebellar volume command but seems to be underestimating volumes despite changing the -n value to attempt best fit. Any suggestions?
> >
>
>
>
> --
>
> Dr Stuart Currie
> BSc, MB ChB, MRCS, FRCR
> Clinical Research Fellow/Honorary Neuroradiology Fellow
> Academic Unit of Radiology
> University of Sheffield
> C Floor
> Royal Hallamshire Hospital
> Sheffield
> S10 2JF
>
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