That should be okay. It will be about as good as a 1mm isotropic T2w image.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Darko Komnenić mailto:komnen...@gmail.com>>
Date: Friday, November 9, 2018 at 11:16 AM
To:
I think that --omatrix1 always outputs a dense matrix.
Matt.
From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, November 9, 2018 at 7:15 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, Stamatios
Sotiropoulos
Here is the line from hcp_fix where it uses a 0.7mm mask:
$FSLDIR/bin/fslmaths veins -div `$FSLDIR/bin/fslstats veins -k
${FSL_FIXDIR}/mask_files/hcp_0.7mm_brain_mask -P 50` -mul 2.18 -thr 10 -min
50 -div 50 veins
wb_command -cifti-export-dense-mapping may be useful for getting the voxel
seeds in the correct order (for the surface, you may be able to just use
the file from the HCP Pipelines global/templates/91282_Greyordinates
folder).
I seem to recall that previously we did this in 3 probtrackx runs, and
It is seeds x seeds with tractography initiated from the seeds. It is square
but non-symmetric.
Matt.
From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, November 9, 2018 at 6:37 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, Stamatios
Indeed if you want all to all tractography you can always parcellate after the
fact.
Matt.
From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Friday, November 9, 2018 at 7:01 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, Stamatios
Those are generated by the RestingStateStats pipeline, but were mainly for an
exploratory analysis that didn’t work.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, November 9, 2018 at 12:47 PM
To:
Dear Matt,
In my previous call, I did get a matrix called fdt_matrix1.dot, which is large
(1.33 GB). I guess this is a dense matrix, but then I wonder again, there might
be something wrong there as well with the positioning of the subcortical
structures, since I used them as seeds.
So I could
I don't know how to get probtrackx to output a parcels by parcels matrix,
or even if it can. If the output files are large (meaning they contain
per-vertex and per-voxel tracks), then the ROIs have not helped you.
Making a dense connectome and then parcellating it will definitely work,
and won't
Yes you probably need to have bash instead of a non-bash shell. Perhaps fixing
that will solve the problem. As far as the resolution of the T1w and T2w,
presumably so long as they are the same resolution everything should work. We
have tested on 0.8mm human data and 0.5mm monkey data.
Matt.
We should change that line to use this file:
${StudyFolder}/${Subject}/MNINonLinear/brainmask_fs.nii.gz
Matt.
From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Friday, November 9, 2018 at 7:18 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Jayasekera, Dinal"
So, it gets a little complicated, because you have to be careful about what
order the different sections of seeds were put together in. I don't know
how specifying multiple ROIs to probtrackx works, keeping it simple and
doing a single combined surface ROI that covers all the areas you want is
Dear Timothy,
Exactly, the goal was to have a structural connectome that has the same parcels
as a functional one and covers the whole brain.
The problem with the surface ROI is that I would be missing the subcortical
structures, which I would like to retain. Maybe there is a simpler way of
Dear Tim,
I made the changes you recommended but I continue to receive the same
segmentation error I mentioned before.
Kind regards,
Dinal Jayasekera
PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering | Washington University in St. Louis
There is wb_command -probtrackx-dot-convert which should be able to convert
the fdt_matrix1.dot file, which should allow a better visualization of the
results. I'm not entirely clear on the arguments to your probtrackx
command, or what the actual ROIs you used are, but it looks like they were
Dear Timothy,
Thank you very much for your quick response.
To clarify some points: some ROIs were surface based and some voxel based. To
create them, I followed the steps I outlined along this thread, which I am
summarizing below:
# creating cortical labels
wb_command -cifti-separate
This is the first problem I see in the text you pasted in the email:
Mask and image must be the same size
This looks like it will happen whenever your T1w and T2w are not 0.7mm, as
it specifically uses a 0.7mm mask. Someone else (Matt?) will need to say
how this is supposed to work.
To Whom it may concern,
In this thread:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06276.html
I found a reference to eroded white matter masks for HCP subjects that should
be stored in
MNINonLinear/ROIs/CSFReg.2.nii
MNINonLinear/ROIs/WMReg.2.nii
but after running the
If by "convenient" you mean "not cifti", then wb_command -cifti-separate
will allow you to get gifti surface label files. If you mean "binary
ROIs", use wb_command -cifti-all-labels-to-rois (and then -cifti-separate
if you want them in gifti format).
If you mean "volume files", we do not
Dear HCP experts,
we got some images from a different center, and their T1 MPRAGE has voxel
dimensions of 1mm in all directions, but their T2 image is 0.5mm*0.5mm*1mm.
Would this be fine for structural HCP pipelines, or would it be a problem
that the resolution is different?
Thanks in advance!
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