Also, you need to use something like an MPRAGE as the Main Structural image, rather than the EPI b0 image, which is of lower quality.
Cheers,
Stam
On 14 Sep 2010, at 09:14, Saad Jbabdi wrote:
> Hi Kazu
> You may have passed the wrong FLIRT transformation to probtrackx.
> Please make sure that:
> 1. The transformation from b0 to struct is correct (overlay the result on the structural in fslview)
> 2. You pass to probtrackx the _inverse_ of the above transform (i.e. from struct to b0)
> 3. Your seed/target masks are all in structural space
>
> Cheers,
> Saad.
>
>
> On 14 Sep 2010, at 06:28, Kazu Tanji wrote:
>
>> Hi list,
>>
>> I found the result of PROBTRACKX, fdt_paths.nii.gz, to be apparently misaligned.
>> For Registration I used skullstripped b0 image as the Main structural image.
>> I don't know if this is relevant but before that, I noticed BEDPOSTX had finished too early like in 6 hours.
>> Is there a way to check what is going wrong?
>>
>> Best,
>> Kazu
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
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