Thank you Matt for this expert advice.
I've checked FNIRT registration for this subject, and it seemed fine, to
make sure the high/low intensities in the myelin map were not generated
through poor registration between T1 FSPGR BRAVO and T2 CUBE.
So, which areas are we worried about in particular - the superior
temporal sulcus for example? The patterns in motor cortex and V1 seem to
resemble your images?
We had real problems with inhomogeneity on the 3T GE scanner, but we
applied the PURE intensity corrections and I computed a significant
decrease of the bias field, when comparing those images to T1s without
PURE correction.
Yes, we used a head coil.
Do you think we'd have to bid farewell to a myelin mapping approach with
this data or would you say there is a work-around by doing ROI-analysis
etc.?
Thanks,
Best wishes,
Barbara
On 31/05/2015 20:42, Glasser, Matthew wrote:
Hi Barbara,
Unfortunately those actually look much more like Gaurav’s than the
ones in in Figure 3 of Glasser and Van Essen 2011 (panels B, E, H, K
were from a GE scanner). The issue is that the sulci on the lateral
surface are brighter than the gyri in a noticeable way relative to
what we typically see, which is not something we saw in the NAMIC GE
data or any of our Siemens data over the years. I’m quite puzzled by
this issue, since it the myelin maps used to work on GE and give
comparable results to Siemens. Also, I don’t have any experience with
GE scanners to know what parameters might be creating the issue.
Here is the info that was available for the GE NAMIC data (that was
acquire some time ago now):
The second dataset includes the 10 control subjects (all male, mean
age 42 11 years) from the publicly available Brain Multimodality
dataset from the National Alliance for Medical Image Computing (NAMIC)
(provided by the Psychiatry Neuroimaging Laboratory and the Surgical
Planning Laboratory, Brigham and Women’s Hospital). The data were
acquired on a 3T General Electric (GE) scanner at Brigham and Women’s
Hospital in Boston using an 8-channel head coil and GE’s parallel
imaging technology Array Spatial Sensitivity Encoding Techniques
(ASSET) was used with a SENSE (SENSitivity Encoding) factor of 2. A
T1w spoiled gradient recalled sequence (SPGR; TR 7.4 ms, TE 3 ms,
TI600 ms, 10° flip angle, FOV 256mm256 mm, matrix 256 256, 1 mm
slices) and a T2w extended echo train acquisition (XETA; TR2500 ms,
TE80 ms, FOV 256mm256 mm, matrix 256256, 1 mm slices) were
acquired. Data were downloaded from the NAMIC MIDAS website:
http://insight-journal.org/midas/collection/view/190.
I’d actually be more inclined to suspect that the T2w sequence
difference CUBE vs the XETA might be the cause of the issue. On
Siemens we use a T2w SPACE sequence which has a lot of contrast for
myelin in it (T2w being a bit of a misnomer, as the contrast in the
SPACE is mostly T1 and MT), if the T2w scan were to have less contrast
for myelin, that could reduce the quality of the results. Another
possibility would be if the transmit field is substantially more
inhomogeneous on this GE scanner (which is probably a different model
than the one used for the NAMIC data). Is the transmit done from a
body coil or a head coil for this GE scanner? In the Siemens scanners
we use the more uniform transmit from the body coil, but if the head
coil were used for transmit, it could produce a more inhomogeneous field.
Peace,
Matt.
From: Barbara Kreilkamp <bakk....@googlemail.com
<mailto:bakk....@googlemail.com>>
Date: Sunday, May 31, 2015 at 2:25 PM
To: Gaurav Patel <gauravpa...@gmail.com
<mailto:gauravpa...@gmail.com>>, "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] myelin maps on GE scanner
Hi Gaurav,
Could you please send over a screenshot of what the artifacts look like?
We've acquired 3D FSPGR BRAVO with PURE correction on the GE MR750
Discovery 3T together with 3D CUBE with PURE correction (32 channels).
The images that HCP computed from that for me look very much like the
ones from Matt's publication, Neuroimage 2014 (single subject),
scaling is 4% to 96% (attached).
Please let me know if this helps or if I can help in any other way.
Thanks,
Best wishes,
Barbara
On 30/05/2015 17:53, Gaurav Patel wrote:
Another problem we have been having is artifacts in myelin maps generated from
the T1s and T2s acquired on our GE MR750D 3T magnet. Matt and I looked at this
in December, and found that in our maps there tended to be an artifactual bias
towards increasing T1/T2 ratio towards the center of the brain, leading to
apparent dense myelination depp in sulci and light myelination at the tops of
sulci that were not real. We've been trying to get to the bottom of this
problem since then with no luck, so I'm turning to the list to see if anyone
else has successfully created myelin maps on a GE scanner and would be willing
to share their sequences (or at least parameters). We've traced the problem
(we think) to the difference between the FSPGR that GE scanners use and the
MPRAGE, specifically the inversion pulse that seems to make the FSPGR more
sensitive to B1 receive field inhomogeneity than the MPRAGE (and the T2
sequence, hence the bias in the T1/T2 ratio). We'
ve compar
ed our seq
uence to the one used in the NAMIC dataset obtained on an older GE scanner
that Matt used in his original myelin mapping paper and haven't come up with
any real differences so far. Any help or insight would be appreciated. Thanks!
__________________________
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
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