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.
>>>> ########################################################################
>>>>
>>>> To unsubscribe from the FSL list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>
>>> ########################################################################
>>>
>>> To unsubscribe from the FSL list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>> ########################################################################
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|