I recommend you use the MSMAll aligned, ICA+FIX denoised data and use
wb_command -cifti-average-roi-correlation. You may or may not chose to do
something like global signal regression to clean up residual global artifact in
the data (which ICA+FIX is not designed to remove) depending on if you think
leaving in global signals will create a bigger positive bias than removing the
mean of the RSNs will create a negative bias (or just analyze things both
ways). We are working on a better solution for this issue that does not
require removing the mean of the RSNs when cleaning up global artifact (i.e.
remove the positive bias in connectivity without adding in a negative bias).
You can make a -vol-roi of the hippocampus by extracting it from this file
${StudyFolder}/${Subject}/MNINonLinear/Results/Atlas_ROIs.2.nii.gz. I would
use a -cifti flag for each run of a given subject, but run separate commands
per subject to generate one dense scalar correlation map per subject. You can
then do statistics on these maps (e.g. with the FSL PALM software tool). You
may wish to do the Fisher transform on the correlation maps first with
wb_command -cifti-math “atanh(x)” <output> -var x <input>
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of Lisa Kramarenko
<[email protected]<mailto:[email protected]>>
Date: Wednesday, April 5, 2017 at 4:40 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Help with the group comparison of seed-based FC
Hello dear experts,
I am very new to HCP so I am struggling with a lot of confusion and hope you
can help. I would like to calculate seed-based FC of hippocampus of two groups
(patients/controls) and to perform a group comparison between them. Now I am
not sure about how to proceed. I see two possible ways:
1. I could merge .dtseries.nii files for all the subjects in a group with
cifti-merge to create a group-average dense connectome. However, how do I
extract the connectivity of the seed of interest and how do I I perform
statistical analysis on it?
2. Or, if I understand correctly, I can use -cifti-average-roi-correlation.
However, I am not sure about the inputs. Should I first merge .dtseries.nii
files for all subjects in a group, take this as <cifti-in> and then extract
hippocampus from Atlas_ROIs.2.nii.gz with cifti-separate and use it as
<roi-vol>? Second question is when I managed to run it, what would the output
be and how do I perform statistical analysis on it?
I would be super grateful if you could clarify what the right way is and give
me a short step-by-step of how to do a seed-based group-level analysis.
Thanks a lot!
Lisa
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