Hello,
I am new to the world of fmri and am writing to get some advice regarding field map acquisition and FSL field map prep, for data acquired using the Verio, Siemens Medical System.
As I understand 3 nifti files are expected following use of the Simens fieldmap acquisition sequence: 1 phase map (file one) and 2 echo times making up 2 magnitude image files (files two and three).
It would appear that our scanner saves the phase map, echo1 and echo2 acquisitions into 2 different folders: folder one contains the phase map as 36 dicoms (one file) and folder two contains the magnitude images as 72 dicoms (also as one file). In the magnitude image folder both echo times are recorded but Siemens names the first Echo1 as 1 and the first Echo2 also as 1: so the dicoms in the file are called 1,1,2,2,3,3, 4,4 etc. The physicist who is helping me said we probably can not change this double naming specified by Siemens.
The dicom to nifti converter I am using (dcm2nii gui) recognises there are 72 images in the magnitude folder and only 36 in the phase map folder, but converts both the 36 and 72 into one nifti file each (not the 2 files I expected from the 72 images).
My question is as follows:
1) Is it correct to use this single magnitude nifti, composed of the 2 echo times in Fsl_prepare_fieldmap gui?
2) If this is not correct can I get some advice regarding how to change the acquisition on our scanner in order to get the 3 expected files in one folder ie phase map, echo1, echo2?
In advance many thanks for the time and help.
Marta
|