Hi,
You don't need to use the 0.5mm image for the registration, as any of the MNI images are in the same space and the same transformations (warps or matrices) can be applied using any resolution of the MNI images. Since using the 0.5mm version in the registration takes a long time but without accuracy benefits, we recommend using the default (2mm) version for the registration. However, it will still be able to transform your 0.5mm masks later on.
All the best,
Mark
On 23 May 2014, at 10:44, Jacobs H (NP) <[log in to unmask]> wrote:
> Hi Mark,
>
> Thanks for the information.
> I remember for the FSL course that I can feed in the mat files in probtrackx, but I am now wondering which files to enter in the registration part.
> The T1 is 1mm isotropic, the DTI images are 2mm isotropic and the seeds are in 0.5mm MNI space.
> So, if I open the registration tab in Fdt, should it then:
> - main structural image: feed in the T1 image of each subject (non-betted?)
> - non-betted structural image: feed in the betted T1 of each subject (or the MNI 0.5mm image?)
> - standard space: the MNI 0.5mm image I guess
>
> Is this correct?
>
> Thanks!
>
> Heidi
>
>
> ================================================
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> [log in to unmask]
> www.maastrichtuniversity.nl
> www.heidijacobs.nl
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> ================================================
> ________________________________________
> Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Mark Jenkinson [[log in to unmask]]
> Verzonden: woensdag 21 mei 2014 13:00
> Aan: [log in to unmask]
> Onderwerp: Re: [FSL] Probabilistic tractography
>
> Dear Heidi,
>
> The diffusion calculations (dtifit and bedpost) are performed in the native space, so without any registration. Once these are done and you have registrations done (which can all be done via the GUI) then you can use masks in MNI space when you perform tractography, and probtrack will be able to move the masks between the spaces for you.
>
> All the best,
> Mark
>
>
> On 17 May 2014, at 12:49, Jacobs H (NP) <[log in to unmask]> wrote:
>
>> Hi,
>>
>> I am using Fdt for the first time and want to make sure I am doing it right.
>>
>> So far I have performed the eddy current correction on the DTI data. Then I oriented all the T1's to FSL's standard and applied BET to them.
>> I also applied BET on one of the no diffusion images.
>> But now I am a bit wondering what I should do next.
>>
>> According to the manual I first should do BEDPOSTX before registering the images. But it says: if you are using the GUI. Does this mean, you first have the register if I would use the command line?
>>
>> Furthermore, I would like to measure the probabilistic connectivity between two seeds that are in MNI 0.5mm space (but my DTI data has a voxel size of 2x2x2mm).
>> Should I register the diffusion images to the MNI 0,5mm? Or should I register the seed to the MNI 2mm template?
>>
>> Thanks for helping!!
>>
>> Best
>> Heidi
>>
>>
>> ================================================
>> Dr. Heidi Jacobs
>> Postdoc researcher
>> Faculty of Health, Medicine and Life Sciences
>> School for Mental Health and Neurosciences
>> Division Cognitive Neuropsychiatry and Clinical Neurosciences
>> Alzheimer Center Limburg
>> [log in to unmask]
>> www.maastrichtuniversity.nl
>> www.heidijacobs.nl
>>
>> Dr. Tanslaan 12, 6229 ET Maastricht
>> P.O. Box 616, 6200 MD Maastricht, The Netherlands
>> T +31 43 38 84 090 F +31 43 38 84 092
>> ================================================
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