I would recommend using fslswapdim to reorient data to axial before  
running TBSS. Make sure you don't mess up l-r though!

Cheers, Steve


------------------------------------------------------------------------
Stephen M. Smith,  Professor of Biomedical Engineering
Associate Director,   Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]   http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------

On 21 Dec 2007, at 23:00, "Zhang, Xiaochu (NIH/NIDA) [F]" <[log in to unmask] 
 > wrote:

> Thank you very much for your help!
> I just tried to convert my input data to NIFTI file.
> I found I have two kinds of input files, one is axial orientation  
> (RAI, neurologically), another one is sagitial orientation (ASR,  
> radiologically).
> However, after tbss_1_, I found all sagitial orientation data  
> (radiologically) are wrong in orientation.
> Can tbss_1 read "ASR" data correctly? Should I change all data to RPI?
> Thanks a lot!
>
> -----Original Message-----
> From: Mark Jenkinson [mailto:[log in to unmask]]
> Sent: 2007年12月20日 18:42
> To: [log in to unmask]
> Subject: Re: [FSL] for the orientation of the MNI space
>
> Hi,
>
> How do you know your images are "LPI"?
> If it is an Analyze file then it does not contain this information,  
> and
> the various tools usually have their own fixed (or configurable)  
> default
> options for interpreting the orientation.  This is why the nifti file
> format was created, so that this information could be stored and its
> meaning universally agreed upon.  Hence we encourage people to use
> nifti where possible.
>
> In FSL we have our own technical definition of "radiological" which
> might
> differ from other people's definition, so be careful.  The most
> important
> issue is normally whether the left-right handedness is that same as  
> that
> of the other images that you are using.  If you are using the MNI152
> templates
> that we supply, then these are in an "RPI" convention (equivalent to  
> the
> FSL definition of "Radiological") and will definitely require Analyze
> images
> to be similarly oriented.  If you know that moving along the voxel
> coordinates
> goes in the opposite direction for your Analyze data (i.e. increasing
> the
> x-voxel coordinate moves you in the Right instead of the Left  
> direction)
> then you need to modify your input images (try fslswapdim) before
> using FSL.
>
> I hope this helps.
> All the best,
>    Mark
>
>
>
> On 20 Dec 2007, at 21:28, Zhang, Xiaochu (NIH/NIDA) [F] wrote:
>
>> Thank you very much for fast response!
>> I just checked my data and found something confused me. My input
>> data is ANALYZE files. It showed "LPI" and "Radiologically". Did it
>> mean my input data is uncorrected in orientation?
>> Thanks, again!
>>
>> -----Original Message-----
>> From: Mark Jenkinson [mailto:[log in to unmask]]
>> Sent: 2007年12月19日 18:37
>> To: [log in to unmask]
>> Subject: Re: [FSL] for the orientation of the MNI space
>>
>> Hi,
>>
>> We *strongly* advise you to change the handedness of your original
>> data before
>> using FSL, as the LPI format (which we term "neurologically stored")
>> can cause
>> problems with some FSL commands.  To change the way the data is
>> stored, see
>> the FAQ entry at:
>>    http://www.fmrib.ox.ac.uk/fslfaq/#general_fslorient
>> and run the fslswapdim and fslorient commands for each input file in
>> LPI form.
>>
>> I'm afraid that you will then need to re-run tbss once you've done
>> this, but it is
>> the best way to be sure that your data orientation is OK.
>>
>> All the best,
>>    Mark
>>
>>
>>
>>
>> On 19 Dec 2007, at 23:12, Zhang, Xiaochu (NIH/NIDA) [F] wrote:
>>
>>> Hi Experts,
>>> I just finished my DTI data analysis via TBSS1.1 (FSL 4.0). I found
>>> a very serious problem when I check the orientation of my data.
>>> My input dataset was LPI. Therefore, I supposed my output dataset
>>> should be stored in LPI. However, actually it showed RPI. I also
>>> checked the “MNI152.nii.gz”. It is RPI, too.
>>> I am confused and worried about my data’s orientation. Who
>>> can save
>>> me?
>>> Thanks a lot!
>>>
>>> Xiaochu Zhang Ph.D
>>>
>>> Visiting Research Fellow
>>>
>>> NIH/NIDA-IRP
>>>
>>> 5500 Nathan Shock Drive
>>>
>>> Baltimore MD 21224
>>>
>>>
>>>
>>> Tel: (410) - 550 - 1440 ext. 434
>>>
>>>
>>
>