Hi,

just to add to this: In the paper you referred to the SN seed masks were actually in individual structural space and I used the 'seed space is not diffusion' option in probtrackx. Then -just for illustration- after I had the results of the each individual's connectivity-based segmentation of the SN I registered the respective subregion masks to MNI space to create a group probability map in a common space.
If you have your masks in MNI space, however, you could load str2diff (and vice versa) warpfields in probtrackx. To get those warpfields, registration of the DTI data to MNI space via the individual structural T1-weighted image usually works very well (for instance combining 'FA to struct' and 'struct to MNI' warpfields using convertwarp).

Best,
Ricarda 


On 21 Jun 2012, at 09:36, Saad Jbabdi wrote:

> Hi Rodrigo
> If you follow the instruction in the doc (registration and probtrackx) you will easily be able to run your tracking in MNI space.
> Note that there is no need for you to transform gradient directions etc. into MNI space. All you need is a transformation between MNI and DTI space, that you then feed to probtrackx.
> 
> Cheers
> Saad
> 
> On 20 Jun 2012, at 17:42, Rodrigo Perea wrote:
> 
>> So I was thinking about registering DTI/DWIs to MNI mainly after reading  "Connectivity-based segmentation of SN in human and its implication s in Parkinson's Disease" (Menke et. al 2010). Could somebody give me more information on how the DTI/DWIs was registered? At what stage? My main issue is that as far as I know registration protocols use mainly skull but DTI/DWIs images do not have a good skull resolution (I guess it might have to use the b0 images). Also, I know if the DWIs are registered to an MNI space, how could we change the gradient directions as well. I am assuming that when we derive the DTI, this gradient directions will be off if the DWIs have changes orientation to be registered into MNI-space.
>> 
>> Any help or reference to books/literature/etc will help.
>> Thanks in advance,
>> Rodrigo
>> 
> 
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
> 
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466  (fax 717)
> www.fmrib.ox.ac.uk/~saad
> 

-----------------------------------
Ricarda A. L. Menke, PhD
FMRIB Centre 
John Radcliffe Hospital
University of Oxford
phone: +44 1865 222797