[Neuroimaging] Two (beginner) questions for DiPy

[Ariel Rokem]

Hi Benedikt,

On Mon, Jan 30, 2017 at 11:20 PM, Wiestler, Benedikt <b.wiestler at tum.de>
wrote:

> Dear Ariel,
>
>
>
> thank you very much for your very helpful reply reg. B-Matrix rotation!
>
> Could you also point out to me how I input a 4D DTI stack (B0 first, then
> some B1000s) for affine co-registration?
>
>
That requires a bit more code. I wrote something in that direction here:
https://github.com/yeatmanlab/pyAFQ/blob/master/AFQ/registration.py#L342-L391,
but I haven't had a lot of opportunities to test/tweak this. Feel free to
use that as a starting point.

Cheers,

Ariel

> Cheers,
>
>
>
> Benedikt
>
> ---
> Dr. med. Benedikt Wiestler
> Abteilung für Neuroradiologie
> Klinikum rechts der Isar, TU München
> Ismaninger Str. 22
> 81675 München
> ------------------------------
> *From:* Neuroimaging <neuroimaging-bounces+b.wiestler=tum.de at python.org>
> on behalf of Ariel Rokem <arokem at gmail.com>
> *Sent:* Monday, January 30, 2017 23:04
> *To:* Neuroimaging analysis in Python
> *Subject:* Re: [Neuroimaging] Two (beginner) questions for DiPy
>
> Hi Benedikt,
>
> On Mon, Jan 30, 2017 at 2:48 AM, Benedikt Wiestler <b.wiestler at tum.de>
> wrote:
>
>> Dear all,
>>
>> first of all thank you very much for making DiPy publicly available.
>> I am new to Python and diffusion imaging (I have worked before with R and
>> genetics), and have two (hopefully easy) questions:
>>
>> 1) As input, I have a 4D nifti image with my B0 and B1000 images stacked.
>> How can I run an affine registration (for motion / eddy correction) on this
>> stack, using the first B0 image as fixed image and the remaining images
>> (one after another) as moving images? Or do I have to split the stack first?
>> 2) How do I rotate the B-matrix after registration?
>>
>
> This function will do that: https://github.com/nipy/
> dipy/blob/master/dipy/core/gradients.py#L265
>
> Cheers,
>
> Ariel
>
>
>> Thanks a lot!
>>
>> Benedikt
>> --
>> Dr. med. Benedikt Wiestler
>> Abteilung für Neuroradiologie
>> Klinikum rechts der Isar, TU München
>> Ismaninger Str. 22
>> 81675 München
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
>
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