Dear FSL experts (Jesper?)
I've spent a bunch of time reading the archives, and while this topic has been discussed frequently, I can't find the answer for my particular application.
I have a group acquiring (for a variety of goals and constrained reasons) BOLD scans with coronal acquisition, FH phase encoding, GRAPPA = 2, and to cut down on terrible phase-wrapping, I put in a reduced phase FOV and phase oversampling. (They preferred all this to RL phase encoding.)
In addition, they have a pipeline that uses conventional dual-echo field maps and fugue; but as the dual-echo maps are badly corrupted by phase-wrap ghosting; I turned to spin-echo field maps for them. However, as the field map goes into fugue, we have to get the readout duration correct.
Is it safe enough to simply use the BW/Pix in the Phase encode direction from DICOM field 0019,1028 to get this value correct? (Or close enough)
eg (from a Siemens Prisma scanner):
FOV 211mm, FOVph = 77.3%
Matrix size 88 x 68
Phase oversampling = 58%
68 rows x .58 = (round up) 40; so total 108 phase-encode "rows"
echo spacing on Sequence Part 1 tab = 0.59ms
effective echo spacing (due to GRAPPA R=2) = 0.295ms
BW Pix PE = 31.387 (from DICOM header implies 1/31.387 = 31.8 ms total readout train length)
actual echo spacing = 1/(31.387 x (68+40)) = 0.295 ms (Implies 108 rows is correct?)
So, readout duration = .295 x (68+40 -1) = 31.56ms
Does this seem correct?
Also, having come across a little gem about the 3 columns in the acqparams file in the list archives.... the -1 and 1 go in the second column as the second dimension of the nifti file has the phase encode direction (dim2 = 68); and this has nothing too do with the scanner coordinates (phase encode principally along z-axis in the scanner, aside from AAScout-induced variations)??
Thanks,
--
Ross Mair
Center for Brain Science
Harvard University
52 Oxford Street
Cambridge, MA 02138
USA
email: [log in to unmask]
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