Print

---

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
>
>
>
>
>
>
>
>
>
>
>