[Mristudio-users] Philips gradient table

[Mojdeh Zamyadi]

Thanks for the detailed reply :) ... I'm using the newest version of 
dcm2nii and the gradient table I'm getting are different (some slightly 
and some more!), so I'm guessing this means dcm2nii is correcting the 
gradients based on patient orientation then?


On 01/08/2014 09:31 AM, Hangyi Jiang wrote:
> usually, with overplus=on, the gradient has to be adjusted based on patient orientation which is recorded in the DICOM header or Philips .par file.  in other words, scanner will apply the original gradient on the patent. this gradient is defined in scanner's coordinate system. but, for tensor calculation, a gradient based on image's system is required.  so, the  original gradient has to be recalculated according to  patient orientation... an extra step before the gradient being applied for tensor calculation .
>
> dcm2nii will get the gradients for DICOM header. the question is, is this gradient in scanner's system or image's system? there is no clear answer here.  it depends on your DICOM files and dcm2nii's version as my knowledge and experiences:  the old Philips DICOM files save the original gradient, some new versions save the adjusted gradients;  old dcm2nii get the gradients directly as this, but some dcm2nii will adjust the gradients using  patient orientation (and some dcm2nii can output the gradient in column format, not row format as you have)... it is quite confusion in practice...
>
> so, we usually recommend that using overplus=off if possible.
>
> for your case, you can try to use dcm2nii for several data set (acquired by same imaging protocol), and check if there is difference between different subject of their gradients.  as we known,  the patient orientation is different in general.  if you find the gradients are different (usually a slight difference) between subjects,  the gradients are good to use.   if not, you may need to adjust the gradients before tensor calculation.
>
> hope it helps,
>
> best,
>
> hangyi
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> extracted from DICOM header is usually the original one (defined in scanner's coordinate system).
>
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> ________________________________________
> From: Mojdeh Zamyadi [mojdehzm at gmail.com]
> Sent: Tuesday, January 07, 2014 4:18 PM
> To: Hangyi Jiang; mristudio-users at mristudio.org
> Subject: Re: [Mristudio-users] Philips gradient table
>
> is there any other (easier) way to do it? the way I do it now is running
> dcm2nii on my dicom files to get the bval and bvec files, but I also
> have to transpose the table since MRIstudio format is not consistent
> with MRIcron. Could you please explain what do you exactly mean by
> recalculating the table?! I thought what's in the .dcm file header is
> the correct gradient, am I wrong?
>
>
>
> On 01/07/2014 04:04 PM, Hangyi Jiang wrote:
>> if dcm2nii works for your case, use dcm2nii.
>> In general, use "overplus = on",  you may need to recalculate the table based on the imaging angles.
>>
>>
>> hangyi
>>
>>
>>
>> ________________________________________
>> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Mojdeh Zamyadi [mojdehzm at gmail.com]
>> Sent: Tuesday, January 07, 2014 2:49 PM
>> To: mristudio-users at mristudio.org
>> Subject: [Mristudio-users] Philips gradient table
>>
>> Hi all,
>>
>> I want to perform tractography on subjects scanned using both 1.5 and 3
>> T Philips scanners (using 15 gradient directions). My question is should
>> I use the gradient table provided on the DTIstudio list or should I use
>> a software like dcm2nii to get the gradient table for each subject and
>> then copy that to DTIstudio? Please also note that the "Gradient
>> Opverplus" option was on at the time of scanning.
>>
>> Thanks a lot,
>> -M
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