[FieldTrip] Format for ft_volumewrite?

[Johanna Zumer]

I'm not familiar with the buffer, but if you can read in your data
successfully, then to convert it to the structure that ft_volumewrite
wants, you can get some information inside ft_datatype_volume for what are
required or optional fields.




2013/5/24 Andrew Brooks <andmib at gmail.com>

> Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
> pull a single volume from the buffer using ft_read_data, and then write it
> out to a nifti file using ft_volumewrite, but ft_read_data does not output
> the volume in a structure that ft_volumewrite wants.
>
>
> On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer <
> johanna.zumer at donders.ru.nl> wrote:
>
>> Dear Andrew,
>>
>> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
>> hopefully the format will match what ft_volumewrite wants.
>>
>> Cheers,
>> Johanna
>>
>>
>> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>>
>>>  Hello all,
>>>
>>> I am new to FieldTrip, so this is a very basic question I was hoping
>>> someone might know an answer to.
>>>
>>> I am using ft_read_data to read the first EPI volume after dummy scans
>>> are thrown out. I want to write this volume to a .nii file to my disk. For
>>> some reason, I am unable to figure out the correct structure that
>>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>>> seem to work. Does anybody have any suggestions?
>>>
>>> [ For a longer explanation of exactly what I am aiming to do, in case
>>> you have any suggestions: I have ROI that is defined in Talairach space.
>>> This is the ROI I would like to pull my real-time data from for each
>>> subject in my study. To do this, I plan to register a talairach template
>>> brain to individual subject-space, and then apply that transformation to my
>>> ROI so that it is in subject space. I was going to simply write out the
>>> subject's EPI to an .nii file, and then run SPM's co-registration step
>>> which allows for a 'child dataset' to be set (my ROI), with the source file
>>> being the template, and the reference being the individual ROI].
>>>
>>> Thanks
>>> Andrew
>>>
>>> _______________________________________________
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>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
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>
>
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