Thanks for fast response. I tryed your command it was also mentioned in a practical paper, but nothing happens, it gives this error massage;
ozgun@linux-iwb0:~/AnV/FAST> fslroi Con1_brain_pve_0.nii.gz Con1_Ventricles 'fslstats Ventricle_XFM_structural.nii.gz -w'
Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
fslroi <input> <output> <tmin> <tsize>
fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.
Any ideas?
All the best
Ozgun
2012/8/25 Saad Jbabdi
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Hi
You can combine fslroi with fslstats -w :
fslroi T1image T1cropped `fslstats VentriclesMask -w`
Saad.
On 25 Aug 2012, at 17:24, özgün özalay wrote:
> Dear FSL experts;
>
> I want to crop my CSF segmented T1 image using a mask to isolate lateral ventricles. fslroi command involves cropping structural images but arguments are x-y-z coordinates. How can i get this mask to extract lateral ventricles?
>
> All the best
>
> Ozgun
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
