Hi,
I'd just like to say that I agree with all of this.
As long as the labels are correct then it will all work fine within FSL, but it might be safer to convert to a consist orientation if you were going to use any non-FSL tools.
All the best,
Mark
On 11 Jan 2013, at 15:13, Michael Harms <[log in to unmask]> wrote:
> Yes, you should be fine, although if want to put your mind at ease by
> getting the nifti's in a consistent fashion, there is certainly no harm in
> that. (And might save you much headache down the road if you end up using
> non-FSL tools with the data).
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: [log in to unmask]
>
>
>
>
> On 1/11/13 9:07 AM, "Anders Hougaard" <[log in to unmask]> wrote:
>
>> Hi Michael,
>>
>> Thanks a lot, that's very reassuring.
>>
>> I have a gut feeling that it would be best to use only one of these
>> two kinds of output in the same analysis, if anything just to avoid
>> confusion.
>>
>> But it should be ok to combine these output types in one analysis
>> (following registration to a template) if the orientation labels are
>> correct?
>>
>> All the best,
>> Anders
>>
>>
>> 2013/1/11 Michael Harms <[log in to unmask]>:
>>> It sounds like the Philips scanner and dcm2nii are simply saving the
>>> nifti's with a different orientation convention.
>>> Mark Jenkinson always says that as all long as the labels are correctly
>>> displayed in 'fslview', then the issue of "neurological" vs.
>>> "radiological" orientation (i.e., "handedness") is irrelevant to all FSL
>>> tools.
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>>
>>> -----------------------------------------------------------
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave. Tel: 314-747-6173
>>> St. Louis, MO 63110 Email: [log in to unmask]
>>>
>>>
>>>
>>>
>>> On 1/10/13 2:57 PM, "Anders Hougaard" <[log in to unmask]> wrote:
>>>
>>>> Dear all,
>>>>
>>>> The Philips Achieva scanner at our site can output data in Philips
>>>> par/rec and/or in nifti-1 format.
>>>> If I use fslorient -getorient to see the orientation of the nifti
>>>> output, fslorient tells me that the files are in neurological
>>>> convention.
>>>> However, if I convert the par/rec output using DCM2NII (part of
>>>> Mricron) to nifti, the files are in radiological convention in FSL.
>>>> The orientation labels are correct in both cases.
>>>>
>>>> How can this be?
>>>> I guess that it would not be wise to use scanner output nifti and
>>>> par/rec converted to nifti combined in the same analysis. Is it
>>>> possible to change the orientation information in the header without
>>>> flipping the image?
>>>>
>>>> All the best,
>>>> Anders
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