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Saad, thank you very much for your answer.

I did step 3 because i thought it was needed the *standard2diff.mat output
from registration. I didn't notice that Flirt created itself the matrix. Do
i have to use this .mat matrix from Flirt in the option: "Select Seed for
diff transform" in Probtrackx?*

**Also, i have tried to use fslstats -thr and -mas but:

1) Which threshold is good to use?
2) When common mask was created i would like to know a percentage value, how
can i obtain it?

Cheers,

Patricia.

2011/1/31 Saad Jbabdi <[log in to unmask]>

> Hi Patricia
>
> Comments below.
>
> > I have some questions concerning to probtrackx tractography. The steps i
> am carrying out are:
> >
> > 1) Flirt each original data in my sample (after eddy_current_correction
> and bedpostx) to the standard MNI152_T1_2mm_brain image.
>
>         You mean register e.g. the b0 image of each subject to MNI space,
> not the whole data? yes that's ok.
>
> >
> > 2) Then i create a mask in the Flirted image of each subject.
>         ok.
>
>
> >
> > 3)  Registration each image to the MNI152_T1_2mm_brain image.
>         not sure what you mean here. Haven't you done this in step 1?
>
>
> >
> > 3) After that i run probtrack with this mask and the matrix converter
> standard2diff.mat
>         ok.
>
>
> > 4) The outputs are fdt_paths.nii.gz of each subjetc
>         yes, and these should be in MNI space.
>
>
> >
> > (I would be glad if you confirm that this process is correct).
> >
> > My question is if is it possible to obtain an unque image which contains
> the % of the paths whose traces match in all the sample and how to get this
> value.
>
> If you mean that you want to consider samples that are common across
> subjects, you could for example threshold the fdt_paths and consider only
> the intersection across subjects.
> You can do these things with fslmaths ( options -thr and -mas )
>
> Saad.
>
> >
> > Thanks for yor attention,
> >
> > Patricia.
> >
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466  (fax 717)
> www.fmrib.ox.ac.uk/~saad
>