I'm guessing you meant 3d nifti rather than 4d.
Anyway, sounds like you're using dcm2nii to convert. The o file is an
automatically reoriented version and the co is an automatically cropped
version of the o image. I have these options disabled in my dcm2nii.ini
file so it's been a while since I used them. Maybe it has changed in recent
versions of dcm2nii but I used to find that the automatic cropping tended
to be overly aggressive, and often chopping part of the cerebellum.
By the way, you can achieve the same effect using fsl tools on the original
file (fslreorient2std and robustfov) which is what I prefer.
On Saturday, November 16, 2013, kavita singh wrote:
> Dr. Smith,
> Thankyou for your prompt reply.
> On Nov 16, 2013 9:18 PM, "Stephen Smith" <[log in to unmask]<javascript:_e({}, 'cvml', [log in to unmask]);>>
> wrote:
>
>> Hi - I *think* they are all basically the same - so keep whichever seems
>> to have the most useful orientation set. Steve.
>>
>> --------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington,
>> Oxford. OX3 9 DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] <javascript:_e({}, 'cvml', [log in to unmask]);>
>> http://www.fmrib.ox.ac.uk/~steve
>> ----------------------
>>
>> On 16 Nov 2013, at 15:38, kavita singh <[log in to unmask]<javascript:_e({}, 'cvml', [log in to unmask]);>>
>> wrote:
>>
>> Hello list,
>> Please forgive if I am asking very basic question as I am new to FSL. I
>> have T1 MPRAGE, 176 dicom images from siemens 3.0 T scanner. When I convert
>> it to 4d compressed nifti, I get 3 files with .nii.gz extension. The
>> prefiix in the files are 'co', 'o' and no prefix. My question is, which
>> file do I need to keep in my FSL_VBM directory?
>>
>> Any help will be highly appreciated.
>>
>> Regard
>>
>> --
>> Kavita Singh
>> Ph. D Scholar
>> NMR Research Centre
>> INMAS-DRDO
>> Delhi-54.
>> skype:livekavita123
>>
>> http://www.linkedin.com/profile/view?id=116620043&trk=nav_responsive_tab_profile
>>
>>
>>
>>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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(716) 859-7677
