As an aside, how old is this particular Trio data? If it is from a VB13
scanner then you should be aware that the bvec information encoded in the
DICOMs is occasionally outright wrong under VB13. Under VB15, the
*polarity* of the bvec stored in the DICOM is sometimes wrong. It wasn’t
until VB17 that the bvec information stored in the DICOMs is entirely
reliable.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: [log in to unmask]
On 4/28/16, 11:01 AM, "FSL - FMRIB's Software Library on behalf of Bastian
David" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Dear FSL-Experts,
I inherited an older DTI dataset and I am stuck with the preprocessing at
the moment. The dataset (recorded on a Siemens Trio 3T) consists of 60
directions and 6 b0's, the bvecs are oriented in a half-sphere and only
one PE-polarity was used in the acquisition (A>>P), so unluckily for me
the opposite of everything you recommend to pay attention to during
acquisition ;) Therefore, I cannot use topup for susceptibility distortion
correction. For most of the subjects I simply run the most recent
implementation of eddy - the FA maps after dtifit look alright.
Nevertheless, during the acquisition somebody had the glorious idea of
recording a gradient field map for the last 10 subjects, which I
understand to be another approach of tackling susceptibility distortions.
My question is: how?
What I have done so far is preparing the field map using
fsl_prepare_fieldmap. For the next steps, I found some old code of Matt
Glasser (
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=FSL&D=0&P=454499
). Adapting these few lines led to warping of the DTI data, that doesn't
seem correct (see attached screenshots). Furthermore, I attached a
screenshot of the flirted field map and magnitude image. Do you have any
idea about what might have gone wrong or how I could proceed? I am very
grateful for every advice!
Greetings from Germany,
Bastian
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