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Just copy-paste the following command, it should work fslroi Con1_brain_pve_0 Con1_Ventricles `fslstats Ventricle_XFM_structural -w` On 25 Aug 2012, at 17:57, özgün özalay wrote: > Dear Saad: > > Yeah i couldn't notice that, sorry but nothing changed. The same error message :) > I can view my mask (Ventricles_XFM_structural.nii.gz) over my structrural T1 scan (Con1_brain_pve_0.nii.gz) in fslview and everything is ok there. > > Still got some ideas? > > All the best > Ozgun > > 2012/8/25 Saad Jbabdi <[log in to unmask]> > Notice that I have used inverted quotes `blah blah` and not 'blah blah' > > saad > > ' > > On 25 Aug 2012, at 17:45, özgün özalay wrote: > >> Dear Saad; >> >> 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 <[log in to unmask]> >> 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 >> > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.fmrib.ox.ac.uk/~saad > > > > > > > > > > > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad