On Wed, Aug 2, 2017 at 6:02 PM, James Morrow
<james.mor...@monash.edu <mailto:james.mor...@monash.edu>> wrote:
Thanks Tim and Matt for the detailed responses.
I agree that mapping to volumes is sub-optimal. Our goal is
to identify coords to be used as targets for brain
stimulation with TMS. We need MNI coords for neuronavigation.
Given the extent of the TMS field, we have some tolerance for
imprecisions in the mapping.
I see. We generally get asked these questions in the context of
fMRI analysis, hence our reluctance.
How does the neuronavigation go from MNI coordinates to subject
coordinates, do you happen to have a reasonable T1w MRI scan of
your subjects? I don't know how big the TMS field is, and I
hadn't looked at the distance from subject to group average
surfaces before, but in one of the HCP subjects, I got a maximum
of 2cm distance from the group average surface (using
midthickness surfaces), which occurred in a few specific
locations, while 90% of the surface was 1cm distance or less.
Can I clarify – was the ICA run on the volumes and then later
mapped on to surfaces, or was it performed on the surface
data? If the former, are the original volumetric results for
the ICA of each subject available anywhere in .nii format?
Cheers,
James
*James Morrow*
Research assistant
Brain & Mental Health Laboratory
*Monash Institute of Cognitive and Clinical Neurosciences*
School of Psychological Sciences
Monash University
c/o MBI, 770 Blackburn Road
Clayton VIC 3800
Australia
T: 03 9902 9768
E: james.mor...@monash.edu <mailto:amy.al...@monash.edu>
www.med.monash.edu.au/psych/bmh/
<http://www.med.monash.edu.au/psych/bmh/>
<http://www.med.monash.edu.au/psych/bmh/>
<http://www.monash.edu/neuro-institute/>
On 3 August 2017 at 07:00, Timothy Coalson <tsc...@mst.edu
<mailto:tsc...@mst.edu>> wrote:
As Matt said, "MNI coordinates" of functionally-aligned
cortical surface features don't have much meaning,
similar to how T1w-aligned MNI space volumes don't have
good cortical functional alignment (except in a few
low-variability regions). We have shown that group
average surface coordinates do not follow the MNI
cortical ribbon (see attached image that simply shows the
average white and pial contours on top of the MNI
nonlinear template). The ICA maps themselves are also
more informative than just the vertices at their peaks.
Surface group results should not be turned into
volumetric files, group average surfaces do not have much
folding left in them, and as such they do not match the
MNI template anymore - this is due to folding
incompatibilities between subjects, but also due to using
functional surface registration instead of folding
patterns. Using the individual surfaces to map to the
volume and then averaging across them would spread your
data out just as badly as doing volume-based analysis of
cortex, so this is also highly discouraged.
Despite strongly advising you not to do what you
outlined, I will tell you what commands you would need.
The -cifti-extrema command will output a map with 1s and
-1s at each local extrema. The surface it uses is for
neighbor information and distance computation - this
isn't as critical as coordinates are, as it merely sets
the maximum possible density of extrema (what you could
get from a very noisy map). You will need to use a
threshold or other method to exclude local extrema that
are outside the high-valued area. We use midthickness
surfaces for this kind of thing (and when doing some
important spatial operation, we use corrected vertex
areas to compensate for the loss of folding in group
average surfaces, see -metric-smoothing).
You can extract the coordinates of a surface file with
-surface-coordinates-to-metric, and you can use
-cifti-separate on the -cifti-extrema result to get those
as metric files, so that the indices will match, so that
you can use them in matlab or some other tool for ad-hoc
analysis (alternatively, use
-cifti-create-dense-from-template to put the surface
coordinates into a cifti file). Since we advise not to
do this with any group data, you are on your own here
(finding the coordinates in a bunch of individuals and
averaging those will give exactly the same bad answer,
reflecting the fact that many/most functional areas have
notably different MNI coordinates in each individual).
Tim
On Tue, Aug 1, 2017 at 7:46 PM, James Morrow
<james.mor...@monash.edu
<mailto:james.mor...@monash.edu>> wrote:
Hi,
We have recently downloaded the HCP900 Parcellation +
Timeseries + Netmats (820 Subjects) dataset.
We would like to obtain the MNI coordinates of
cluster peaks in the melodic_IC.dscalar.nii ICA maps.
Is there any way to do this?
Is the –cifti-extrema function of wb_command the
correct command? It requires a surface file, but I’m
not sure which would be most appropriate for the
group ICA results.
Alternatively, would there be a way to convert the
dscalar file into a standard volumetric nii so that I
can use standard FSL tools?
Thanks
James Morrow
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