Yes. That is correct.
Regards,
Divesh Thaploo
Smell and Taste Clinic
Dept of ORL, Carl Gustav Carus
TU Dresden, Germany
+49 177 4236 487
Skype-ID: dthaploo
On Thu, Mar 12, 2020 at 2:34 PM Renew Andrade
<[log in to unmask]> wrote:
>
> May be the problem is that I have acquisition_parameter.txt with 0 1 0 1 Is that ok?
>
> > On 12 Mar 2020, at 14:32, Divesh Thaploo <[log in to unmask]> wrote:
> >
> > Hello
> >
> > I think that should work provided the numbers are same throughout the subjects.
> >
> > Regards,
> > Divesh Thaploo
> > Smell and Taste Clinic
> > Dept of ORL, Carl Gustav Carus
> > TU Dresden, Germany
> > +49 177 4236 487
> > Skype-ID: dthaploo
> >
> > On Thu, Mar 12, 2020 at 2:30 PM Renew Andrade
> > <[log in to unmask]> wrote:
> >>
> >> I have seen now that you can look for this number in Siemens some how comparing with images given in another part of the tutorial. But I cannot find for sure which MRI was used for my dataset. Does it alter too much if I made up the numbers.
> >>
> >>
> >>> On 12 Mar 2020, at 13:54, Divesh Thaploo <[log in to unmask]> wrote:
> >>>
> >>> Hello Andrade
> >>>
> >>> You need the echo spacing(ms), EPI factor and phase encoding. Then you
> >>> can get the numbers in acq file.
> >>> See here,
> >>>
> >>> The --acqp file is of the same format as the --datain parameter for
> >>> topup, and quite possibly you can re-use the one you created for
> >>> topup. It is used to inform eddy what direction the distortions are
> >>> likely to go in. Each row consists of a vector (three values) that
> >>> specify what the phase-encode (PE) axis is and also what direction
> >>> along that axis that imply higher frequency. So for example the two
> >>> lines
> >>>
> >>> 0 1 0 0.085
> >>> 0 -1 0 0.085
> >>>
> >>> have the vectors [0 1 0] and [0 -1 0] which both imply that PE is
> >>> along the y-direction and which further imply that for the first row
> >>> [0 1 0] a higher frequency is associated with a position higher up
> >>> along the y-direction (i.e. positive blips) and the second [0 -1 0]
> >>> implies that a lower frequency is associated with a position higher up
> >>> (i.e. negative blips).
> >>>
> >>> The fourth element in each row is the time (in seconds) between
> >>> reading the center of the first echo and reading the center of the
> >>> last echo. It is the "dwell time" multiplied by "number of PE steps -
> >>> 1" and it is also the reciprocal of the PE bandwidth/pixel.
> >>>
> >>> For a Siemens scanner you will get a "protocol PDF" that contains all
> >>> the relevant information. Look for the tags "Phase enc. dir.", "Echo
> >>> spacing" and "EPI factor". Here is an example
> >>>
> >>> Phase enc. dir. A >> P
> >>> ...
> >>> Echo spacing 0.8 [ms]
> >>> ...
> >>> EPI factor 128
> >>>
> >>> Where the first tag tells us that more posterior (lower down in the
> >>> y-direction) locations are associated with higher frequency meaning
> >>> that our vector should be [0 -1 0] and where the second two tags tells
> >>> us that the fourth number should be 0.8*0.001*127=0.102 resulting in
> >>>
> >>> 0 -1 0 0.102
> >>>
> >>> as the row for our --acqp file.
> >>>
> >>> I am afraid that I don't have sufficient experience of the other
> >>> scanner manufacturers to know how/where the relevant information is
> >>> stored.
> >>>
> >>> Regards,
> >>> Divesh Thaploo
> >>> Smell and Taste Clinic
> >>> Dept of ORL, Carl Gustav Carus
> >>> TU Dresden, Germany
> >>> +49 177 4236 487
> >>> Skype-ID: dthaploo
> >>>
> >>> On Thu, Mar 12, 2020 at 12:55 PM Renew Andrade
> >>> <[log in to unmask]> wrote:
> >>>>
> >>>> Dear FSL experts:
> >>>>
> >>>> I cannot find a way to understand how to fulfil the data that goes in acquisition parameters txt file in topup for dti processing. I have read the tutorial but it doesn’t show how the numbers are obtained. Is it something from the MRI. I am working with data obtained through repositories. And I have no more than bvalues bvectors and “nii.gz" images.
> >>>>
> >>>> Sincerely,
> >>>> Andrade.
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