Hello Matt and HCP Community,
Thank you for the helpful e-mail and words of encouragement. We are very
encouraged by the data / results we can view in the Connectome Workbench;
however, statistical analysis has proved challenging.
Just to reiterate what we are attempting to do: we are hoping to compare
whole-brain (all ~91k brainordinates) connectivity between two predefined
brainordinates to determine the areas of the brain in which there is a
statistically significant difference in connectivity. We intend to eventually
extend this analysis to compare two different ROIs (sets or masks of
brainordinates); however, for simplicity's sake (and to prove to our PI that we
can do this) we would like to perform this comparison first between two voxels
/ vertices (henceforth brainordinates "A" and "B").
The general pipeline (using the 33 GB resting state dense connectome CIFTI file
as our starting point) is as follows step-by-step:
1. Reduce the resting state dense connectivity CIFT file (91k x 91k) into
two separate CIFTI files, which are NOT dense. These CIFTI files ("A" and "B")
would contain the whole-brain connectivity data from two a priori specified
brainordinates ("A" and "B"). By size, these intuitively should be around 91k
in number of brainordinates. We are not exactly sure how to best achieve this
in wb_command... would "CIFTI-parcellate" do the trick? Or, can we read the
CIFTI data into MATLAB and simply select an individual row corresponding to the
brainordinate of interest? If you have any thoughts as to the most direct way
to do this, it would be appreciated.
2. Apply "CIFTI-separate" to both CIFTI files A and B. This should result
in two 2D surface maps (for the left and right hemispheres) in NII format for
both brainordinates "A" and "B", along with their corresponding GIFTI files to
register them in space. A single 3D volume map of the subcortical / cerebellar
brainordinates should also result from this for both brainordinates "A" and
"B". So, we end up with 6 NIFTI maps and 4 GIFTI files.
3. Apply FSL PALM with TFCE correction (syntax similar to randomize) to each
of the three pairs of maps produced in #2 (left cortex, right cortex, and
subcortical) to compare "A" versus "B." We will need to include the
midthickness file as an argument for the 2D surface data, in order for PALM to
appropriately correct for volume. This should result in three "A > B" contrast
maps (left cortex, right cortex, subcortical).
4. Use wb_command to reconstruct whole brain CIFTI files from the three
contrast maps produced in #3, which can then be viewed in Connectome Workbench
for inspection. We hope that this will provide areas of the brain in which
connectivity between brainordinate "A" and "B" are significantly different,
with the appropriate correction for multiple comparisons in #3.
Any comments / suggestions / heckling would be sincerely appreciated. Thank
you in advance!
Mike
Michael F. Regner, M.D.
Departments of Radiology and Bioengineering
University of Colorado - Denver
E-mail: michael.reg...@ucdenver.edu<mailto:michael.reg...@ucdenver.edu>
From: Glasser, Matthew [mailto:glass...@wustl.edu]
Sent: Monday, July 10, 2017 8:15 PM
To: Regner, Michael <michael.reg...@ucdenver.edu>; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Statistical comparison of whole brain (surface
"voxels" + subcortical / cerebellar voxels) connectivity between two explicitly
defined voxels
Hi Michael,
I'm happy to hear you are making good progress with CIFTI and Connectome
Workbench. You can indeed use the PALM software to do statistical inference on
CIFTI data, and that is the tool we recommend.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Regner, Michael"
<michael.reg...@ucdenver.edu<mailto:michael.reg...@ucdenver.edu>>
Date: Monday, July 10, 2017 at 2:40 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Statistical comparison of whole brain (surface "voxels" +
subcortical / cerebellar voxels) connectivity between two explicitly defined
voxels
Dear HCP Community,
I am relatively new to the HCP data and Connectome Workbench. Our
neuroradiology laboratory at the University of Colorado is beginning to use it.
It has already proved to be extremely helpful in aiding the interpretation of
existing resting state results.
My question is: does the HCP Connectome Workbench provide an internal
mechanism for the generation of statistical comparisons / contrasts within or
between CIFTI files? I am exploring the dense resting state connectivity data.
My goal is to construct a contrast map for statistical inference. I would
like to compare whole brain (surface "voxels" + subcortical / cerebellar
voxels) connectivity between two explicitly defined voxels within the dense
resting state connectivity CIFTI file (or construct new whole-brain
connectivity map CIFTI files for two explicitly defined voxels, and
statistically compare these two maps). So, the desired resultant map / CIFTI
file would illustrate the statistically significant difference in connectivity
between these two points across the whole brain. Is there a way to do this
with "-cifti-math" or the correlation command? As a corollary, can this be
performed in FSL / PALM? This is probably a very basic question, but coming
from years of SPM8 / SPM12 experience it is not very intuitive...
Any comments, suggestions, or pointers would be much appreciated!
Thank you,
Michael F. Regner, M.D.
Departments of Radiology and Bioengineering
University of Colorado - Denver
E-mail: michael.reg...@ucdenver.edu<mailto:michael.reg...@ucdenver.edu>
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