If your gradient directions are specified relative to the magnet's axes (and
for Siemens' default DTI sequence, they are), then they need to be
reoriented if your row, column, and slice directions do not correspond to
the x, y, and z coordinates of your magnet.
Jolinda
Jolinda Smith
Lewis Center for Neuroimaging
University of Oregon
Eugene, OR 97403
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-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Ed Roberts
Sent: Tuesday, June 27, 2006 8:59 AM
To: [log in to unmask]
Subject: [FSL] FA pipeline
Hi,
I'm trying to generate some FA maps to do a regression analysis with, and I
wanted to check whether I was using the right things in the right order.
I'm using a Siemens 1.5T scanner with 12 directions, b-values 0 & 1000.
1. Dicoms from the scanner into SPM to get hdr and img files. 2. All 13
diffusion files into MRICRO to get a 4D data file. 3. Normalise B-vec
values. 4. B0 image into BET to get a no_diff and no_diff_mask file. 5. Run
dtifi.
So, I'm concerned that I'm missing out doing any registration or alignment,
or does this happen in FDT? Apparently the data I need to adjust for the
eddy currents isn't easily available, so I might have to skip that.
Any my other slightly related question is how do I know if Bedpost has
crashed? Is there any good way to tell or do you just have to cross your
fingers and wait?
Thanks,
Ed Roberts
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