Hi,
I'm not 100% sure what you are asking, but out of the options
you present, only number 1 is good. You should not apply
FLIRT to the input or output of FIRST. The first stage in run_first_all
applies FLIRT to do a registration to the MNI152 space, and
then it transfers the model information back into the original
image space. Doing anything else degrades the image quality.
However, if you did want a volume of the structure in standard
space for some reason (not sure why), then you could use something
similar to option 2, although you should extract the structure of
interest
first and then apply FLIRT to the image containing just this
structure alone. Otherwise the interpolation will change the
label values and do something you do not want.
Normally I would expect you to want the volumes of the structures
in the original images, in which case option 1 is definitely the
right thing to do.
I hope this answers your questions.
All the best,
Mark
On 18 Sep 2009, at 09:54, diagnostico imagenes wrote:
>
> Hi Mark, Hi Group!
>
>
> Mark,thank you so much for your help in FIRST! =)
>
> run_first_all is required normalize with MNI152_T1_1mm.nii.gz?
>
> some of these options is correct?
>
>
>
> option 1)
> I run run_first_all -i con01.nii.gz -o output
> and get
>
> output_all_fast_firstseg.nii.gz
> output_all_fast_origsegs.nii.gz
>
> Volumen hipp Left
>
> fslstats output_all_fast_firstseg.nii.gz -l 16 -u 18 -V
>
> Volumen1 --> 3500 mm3 (Approximate) nearby to mean in human normal
>
> or...
>
>
>
>
> option 2)
>
> I run run_first_all -i con01.nii.gz -o output
> and get
>
> output_all_fast_firstseg.nii.gz
> output_all_fast_origsegs.nii.gz
>
> Volumen hipp Left
>
> fsl_flirt output_all_fast_firstseg.nii.gz norm
>
> fslstats norm.nii.gz -l 16 -u 18 -V
>
> Volumen2
>
> or...
>
>
>
>
> option 3)
>
> fsl_flirt con1.nii.gz norm
>
>
> I run run_first_all -i norm.nii.gz -o output
> and get
>
> output_all_fast_firstseg.nii.gz
> output_all_fast_origsegs.nii.gz
>
> Volumen hipp Left
>
>
> fslstats output_all_fast_firstseg-l 16 -u 18 -V
>
>
>
> Volumen3-->4951 mm3 (Approximate) is equal al MNI152_T1_1mm
>
>
> //---------------------------------------------------------------
>
> note MNI152_T1_1mm_all_fast_firstseg--->
>
> fslstats MNI152_T1_1mm_all_fast_firstseg-l 16 -u 18 -V
> 4951 4951.00mm3
>
>
>
>
>
> Thank you so much for your time
> Yours sincerely,Nicolas
> Student of Biomedical engineering
>
> Ingresá a tu Hotmail desde tu Messenger. ¡Windows Live hace tu vida
> más simple!
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