[FieldTrip] Format for ft_volumewrite?

Andrew Brooks andmib at gmail.com
Fri May 24 15:15:09 CEST 2013

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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