Hi Diana and Sergiu,
Because of this thread, I am questioning my analysis method, so I've
posted a question on the Philips MR list. If I get a reply, I'll let
you know.
Also, the Physicist I work with is going to ask his Philips contact,
so I'll let you know about that as well.
Does anyone know what people with other make of scanner does? Do
they generate individual bvec files?
Thanks
Suzanna
On 29 Feb 2008, at 12:31, Diana Tordesillas Gutiérrez wrote:
> Hi,
>
> I have no answeer for your question, but you might be interested to
> ask in
> the Philips MR list. It's a fairly new one. The link is:
>
> http://lists.liu.se/mailman/listinfo.cgi/pmr-users-mail
>
>
> Good luck,
> Diana
>
> S. Groppa dijo:
>> Thanks a lot!
>>
>> What I found out is that in the par file there are 2 parameters for
>> angulation and it should be somehow possible to use these and the
>> original phillips directions to get the final bvecs...
>>
>> but it is not writen somewhere, or I can not find it...
>> but thanks a lot for your help.
>>
>> I'll post a solution if I find smth reasonable.
>>
>> best wishes
>>
>> Sergiu
>>
>>
>>> HI Sergiu,
>>
>>> I'm afraid I don't know about this. I shall forward your email to
>>> the Physicist I worked with, and see if he knows. You could try
>>> sending a question about Phillips scans and bvecs to the list...I
>>> think there's a few people using this make of scanner and FSL, so
>>> someone must know the answer.
>>
>>> There was a long thread about Phillips scans in the archives. I
>>> don't know what it was about, so it may or may not be helpful.
>>
>>> The normalisation is recommended by FSL for all bvecs. It ensures
>>> that each direction in the bvecs has a magnitude of 1. There's an
>>> equation in the FDT section of the FAQs.
>>
>>> Good luck with this, I'll follow your emails with interest.
>>> Suzanna
>>
>>> On 29 Feb 2008, at 06:51, S. Groppa wrote:
>>
>>>> Dear Suzanna,
>>>> Thanks a lot for your answer.
>>>>
>>>> you are right .par .rec is this philips intern format. And
>>>> that's true
>>>> that actually you can get the bvecs from the scanner but because of
>>>> the angulation(I
>>>> hope that's the right word) the values are always slightly
>>>> different
>>>> (as I understood just re-calculated in the patients plain).
>>>>
>>>> In some later versions of the par the values of the bvecs are in
>>>> it,
>>>> in mine not...
>>>>
>>>> ok what about normalization of bvecs, is it alway needed? What
>>>> for? Or
>>>> ist only a par/rec thing.
>>>>
>>>> I thank you very much!
>>>>
>>>> Sergiu
>>>>
>>>> the
>>>>> Hi Sergiu,
>>>>
>>>>> Are you using a Philips scanner for the par/rec files? If so
>>>>> you can
>>>>> get the bvecs from the scanner. I don't know if they're
>>>>> encoded in
>>>>> the par/rec files. You b values will relate to your images, so if
>>>>> you had 32 directions at b=10000 and 2 b=0 images, this forms your
>>>>> bvals file (obviously the order needs to match the bvecs).
>>>>> Also, as
>>>>> a reminder, don't forget to normalise your bvecs, it tells you
>>>>> how to
>>>>> do this in the FAQs on the FSL website.
>>>>
>>>>> Suzanna
>>>>
>>>>
>>>>> On 28 Feb 2008, at 18:13, S. Groppa wrote:
>>>>
>>>>>> Dear list,
>>>>>>
>>>>>> I apologize for this in a way repeated question but I did't
>>>>>> find in
>>>>>> the list a complete answer for it.
>>>>>>
>>>>>> I've just got some *.par *.rec 's data - and tried to convert
>>>>>> it to
>>>>>> fsl_nifti
>>>>>> which functioned quite good (through dcm2nii) - but
>>>>>>
>>>>>> without getting the bvals and bvec??
>>>>>>
>>>>>> with the error message par 4.1 not yet fully supported.
>>>>>>
>>>>>> I tried r2agui with no success.
>>>>>> Any other ideas of becoming the bvals and bvecs?
>>>>>>
>>>>>> thanks a lot and sorry for this never ending story.
>>>>>>
>>>>>> best wishes
>>>>>>
>>>>>> Sergiu
>>>>
>>>>
>>>>
>>>> --
>>>> Mit freundlichen Grüßen
>>>> S. Groppa
>>>> mailto:[log in to unmask]
>>
>>
>>
>> --
>> Mit freundlichen Grüßen
>> S. Groppa
>> mailto:[log in to unmask]
>>
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