[Mristudio-users] Philips gradient table

[Susumu Mori]

that's likely, but I'm not familiar with dcm2nii


On Wed, Jan 8, 2014 at 10:01 AM, Mojdeh Zamyadi <mojdehzm at gmail.com> wrote:

> 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
> >
> >
> >
> >
> >
> >
> >
> >
> > extracted from DICOM header is usually the original one (defined in
> scanner's coordinate system).
> >
> >
> > ________________________________________
> > 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
> >> _______________________________________________
> >> mristudio-users mailing list
> >> mristudio-users at mristudio.org
> >> http://lists.mristudio.org/mailman/listinfo/
> >> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20140108/6e73618b/attachment.html