Nope, you can do the tractography directly from the surfaces using FSL:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces Use the
surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k. White surfaces are
good for counting and pial surfaces are good for stopping. There are
wb_commands you could use if you want to extract ROIs from task fMRI maps.
Will you be using individual subject task fMRI maps or group maps? If it is
individual subjects, I would define the ROIs based on the peak gradient
boundaries of the effect size maps, as these are the biologically significant
functional transitions.
Peace,
Matt.
From: Yin Wang >
Date: Thursday, August 17, 2017 at 12:34 PM
To: "hcp-users@humanconnectome.org"
>
Cc: Matt Glasser >
Subject: help: extract MNI coordinates of tfMRI blobs from workbench
Dear HCP team,
We are interested in using both task fMRI and diffusion MRI data to study white
matter pathways between functional cortical regions. We are planning to use
task fMRI activation to define several ROIs as seeds for dMRI tractography. We
have several questions below and hope someone can help us.
As far as I understand, all tfMRI results (e.g. contrast maps) for each subject
are in grayordinate space (let us only limit the discussion to the cortex), but
the dMRI is volumetric data. That means I have to extract the MNI coordinates
for each ROI from the contrast maps so that I can use them directly for dMRI
tractography. How can I do this procedure from connectome workbench?
1. Usually when I do this in SPM (using traditional volumetric data), I need to
first set up a threshold (e.g. p<0.05 uncorrected) to get the blobs and then
write down their peak coordinates for further DTI analyses. However in the
workbench, I cannot find a button to set a p value. All I can do in workbench
is to manually slide the threshold bar from the Overlay Toolbox (i.e. Overlay
and map settings—Palette--Threshold). What does the value mean in the threshold
map (e.g. are these CIFTI SCALARS t-values or z-scores)? How can I transform it
to the typical p value? Do you know any functions in the workbench that I can
set a fixed threshold across subjects?
2. Let’s assume I now got a blob from certain threshold, how can I get its MNI
coordinates from the workbench? I clicked the blob in the montage view and the
information window gave me some XYZ coordinates. First, which surface should I
use? midthickness, inflated or very_inflated? I found their vertex number for
the same blob is identical but the xyz coordinates in each surface are quite
different? Second, in SPM, the MNI coordinates are integers (e.g. -51, -45, 8),
but why the xyz coordinates provided by the information window have decimal
points (e.g. -51.2555, -45.8909, 8.1537)? Do I just round them up?
3. We are planning to extract each ROI’s MNI coordinates from each individual’s
specific tfMRI contrast maps. That means we have to manually extract values
from the information window for each of 1200 subjects. Are there any automated
scripts (for workbench) that we can use to extract coordinate information from
peak site of a blob (and batch for multiple subjects)?
Sorry for so many questions and we appreciate any helps and advice.
Best
Yin
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