Hi all,
I am a master student of neuroscience and for my thesis I am working on DTI data. The project aims to find correlations between FA values and a creativity factor. The data has been collected in 2011 and the technician who has set the acquisition protocol has moved somewhere else and I have no reference to find out the answer of my questions. I highly appreciate any help. My questions regard to acquisition parameters and bvecs calculation.
In a standard preprocessing pipeline I should first calculate FA image and V1 image. For doing that I need bvecs which I calculate with mricron but the calulated V1 is not aligned with FA. an example can be found in the link below:
http://i67.tinypic.com/6jh5p1.png
1) How can I calculate the correct bvecs?
Next I should correct my images for motions and distortions. As I don't have two images with different phase encoding directions I should use fieldmap which I calculate using Fsl_prepare_fieldmap as the scanner is Siemens. Then I should feed it to fugue but I need dwell time. In my EPI header i find a dwell time like this:
sRXSPEC.alDwellTime[0] and is equal to 2200.
2) Can I use this value? Is this value in micron?
After that I should use eddy. To use it I need acqp text file. I know what it means. about the last column I know that I should multiply my dwell time as above by epi factor - 1.
3) As I have only one PE direction how can I make this acqp text file? What can I put as the second row?
Also about index text file. I have 50 gradient directions.
4) Should I make a text file with 50 1s?
Many thanks in advance!!!
Bests
Arman
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