Okay, thank you to both of you.
Best wishes,
Barbara Anne
On 07/05/2015 03:35, Glasser, Matthew wrote:
That’s a good point and would still be true of the current version of
the HCP Pipelines. While we don’t rely on FNIRT to align cortex, it
is still used to make the initial brain mask, and that could work not
as well without FAT sat. You should probably check over your results
more carefully if not using FAT sat to see if any subjects need to be
excluded (e.g. obvious large very high or very low intensity artifacts
in the myelin maps).
Peace,
Matt.
From: <Harms>, Michael <mha...@wustl.edu <mailto:mha...@wustl.edu>>
Date: Wednesday, May 6, 2015 at 9:30 PM
To: Matt Glasser <glass...@wusm.wustl.edu
<mailto:glass...@wusm.wustl.edu>>, Barbara Kreilkamp
<bakk....@googlemail.com <mailto:bakk....@googlemail.com>>,
"hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Myelin Mapping
Separate from FS, we've also found that fat sat in the T1 helps make
FNIRT more robust.
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: mha...@wustl.edu <mailto:mha...@wustl.edu>
From: <Glasser>, Matt Glasser <glass...@wusm.wustl.edu
<mailto:glass...@wusm.wustl.edu>>
Date: Wednesday, May 6, 2015 11:57 AM
To: Barbara Kreilkamp <bakk....@googlemail.com
<mailto:bakk....@googlemail.com>>, "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Myelin Mapping
Not having FAT saturation is mainly an issue for FreeSurfer which can
sometimes get the surface wrong if it gets confused and thinks fat is
white matter. I don’t know how much of an issue this is for more
recent HCP Pipeline versions though.
Peace,
Matt.
From: Barbara Kreilkamp <bakk....@googlemail.com
<mailto:bakk....@googlemail.com>>
Date: Wednesday, May 6, 2015 at 11:53 AM
To: "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Myelin Mapping
Thanks, Matt, this is great.
You said once 'You will need a T1w and a T2w images acquired in the
same scanning session with the same image intensity filters (e.g. pre
scan normalize or not) applied to both.'
Are these the main issues I have to look out for? As I notice some
differences in my acquisition parameters when comparing to other papers.
Also, we did not apply FAT saturation, I read somewhere this would be
beneficial for myelin mapping.
Best wishes and thanks for your help.
Barbara Anne
On 05/05/2015 23:00, Glasser, Matthew wrote:
(1) Use the 1mm templates.
(2) You can do this, but it’s important to note that the myelin/iron
relationship, which is very close in cortex, may deviate more in
subcortical white matter. Also, the myelin content of a white matter
region will depend on the density of axons vs other things, ratio of
space inside the axon to the space taken up by the myelin wraps, etc,
which may produce counterintuitive effects. Also, while one can
validly do stats on grey matter myelin on the cortical surface, white
matter in the volume is quite tricky (more central regions may be
reasonably aligned with nonlinear volume registration, but more
cortical regions have the same issue as cortical grey matter and
won’t be aligned well). Perhaps a TBSS-like skeleton approach is
warranted…
(3) Have a look at the references in the beginning of Glasser and Van
Essen 2011 Journal of Neuroscience
(http://www.jneurosci.org/content/31/32/11597.short) for the
validation of various MR contrasts vs histological myelin stains.
Also there’s more discussion of this in Glasser at al 2013
Neuroimage, Trends and Properties of Cortex
(http://www.sciencedirect.com/science/article/pii/S1053811913003108).
Peace,
Matt.
From: Barbara Kreilkamp <bakk....@googlemail.com
<mailto:bakk....@googlemail.com>>
Date: Tuesday, May 5, 2015 at 4:46 PM
To: "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Myelin Mapping
Dear Matt and HCP experts,
Thanks again for this.
I have some further questions:
(1) Even if my data is 1x1x1mm^3 should it be registered to the
workbench default T1 MNI of 0.7mm or to 1x1x1mm^3?
(2) Within HCP: Is it valid to also look at white matter myelin not
just cortical myelin?
(3) Finally, does anyone know any postmortem validation studies for
this technique?
Thank you very much,
Best wishes,
Barbara Anne
On 20/02/2015 13:08, Glasser, Matthew wrote:
Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w
myelin maps with the latest code/methods (including bias correction
and normalization):
https://github.com/Washington-University/Pipelines
You will need a T1w and a T2w images acquired in the same scanning
session with the same image intensity filters (e.g. pre scan
normalize or not) applied to both. For myelin mapping only, a field
map is optional (but recommended).
Peace,
Matt.
From: Barbara Kreilkamp <bakk....@googlemail.com
<mailto:bakk....@googlemail.com>>
Date: Friday, February 20, 2015 at 7:04 AM
To: "hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Myelin Mapping
Dear HCP- users,
Could you please point me to a tutorial for myelin mapping with
Human Connectome Workbench software?
Also, is there a way to implement bias-correction for this technique?
Thank you very much,
Best wishes,
Barbara
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