Dear Matt,
Thank you for your reply to my question about myelin mapping.
There was indeed an issue with oblique s- and qforms (for the T2
images) which I resolved.
I discovered for a subject however that still for frontal and occipital
areas t1/t2 ratios were not well mapped (there are large areas that give
values zero). Indeed, when I look at the volume-surface registration in
Caret the areas do not correspond well.
I have several questions and would be very grateful if you could help
me:
1. I wondered if for the original T1 the stereotaxic coordinates should
be set to 0,0,0 for the anterior commissure before running myelin
mapping.
2. Should the original T1 be set in LPI orientation before myelin
mapping or is Caret doing this automatically? Might this be in conflict
with Freesurfer files and how to proceed? And should the original T1 and
T2 be skull-stripped?
3. In the myelin mapping operations it is indicated that images are
best not resampled with trilinear interpolation. However, the
mri_convert rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz command is
actually using trilinear interpolation. Is it possible and necessary to
do mri_convert with spline interpolation?
Thank you very much for your suggestions!
Best,
Ruthger
Le 2014-03-15 18:00, [email protected] a écrit :
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Today's Topics:
1. Re: question about myelin mapping (Matt Glasser)
----------------------------------------------------------------------
Message: 1
Date: Fri, 14 Mar 2014 11:42:29 -0500
From: Matt Glasser <[email protected]>
To: "Caret, SureFit, and SuMS software users"
<[email protected]>
Subject: Re: [caret-users] question about myelin mapping
Message-ID: <cf489b8d.c23b3%[email protected]>
Content-Type: text/plain; charset="ISO-8859-1"
Do the volumes align with the surfaces? Did you remove any oblique
sforms?
Peace,
Matt.
On 3/14/14 8:01 AM, "Righart, Ruthger" <[email protected]>
wrote:
Dear Caret experts,
I am using Caret for myelin mapping and I got first results for 4
subjects.
After loading MyelinMapping.metric in Caret, for some of the subjects
large areas are missing, both for left and right hemisphere,
particularly in the occipital areas (i.e., the metric file seems to
have
missing values, however the corrected thickness metric displays
values
in these areas).
Registration of T2-to-T1 is fine. The ribbon.nii.gz file and the
T1wDividedByT2w_ribbon.nii.gz seem fine as well, though the ribbon in
the occipital areas has fewer voxels than other areas (probably
because
these areas are relatively thin), and I wondered if this may cause a
problem for the final metric data.
The caret_command -myelin-mapping script reports rather high
percentages of missing nodes : ?Out of 113592 cortex nodes, 50.37%
were
zero and needed correction. When reconstructing discarded nodes,
68.88%
were zero and not used?.
Thank you very much in advance for your time, any help would be very
much appreciated!
Ruthger Righart
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