Thanks Tim for clarifications! It was helpful to know that surface
registration is by vertices, not by cifti indices.
Best,
Reza
On Tue, Nov 20, 2018 at 11:48 PM Timothy Coalson wrote:
> Surface registration (whether left/right or otherwise) is by vertices, not
> by cifti indices, and is
Surface registration (whether left/right or otherwise) is by vertices, not
by cifti indices, and is therefore a separate issue from the medial wall
masks (I would bet that the actual mismatches between the two medial walls
is more than 20 vertices - the Venn diagram of the sets of included
Sorry ... I should have said 20 vertices difference.
On Tue, Nov 20, 2018 at 3:52 PM Reza Rajimehr wrote:
> ... 29716 indices in RH and 29696 indices in LH of cifti file.
>
>
> On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr wrote:
>
>> But there are 10 more vertices in right hemisphere than
... 29716 indices in RH and 29696 indices in LH of cifti file.
On Tue, Nov 20, 2018 at 3:43 PM Reza Rajimehr wrote:
> But there are 10 more vertices in right hemisphere than left hemisphere ...
>
>
> On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew
> wrote:
>
>> Left and right are registered.
But there are 10 more vertices in right hemisphere than left hemisphere ...
On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew wrote:
> Left and right are registered.
>
> Matt.
>
> From: Reza Rajimehr
> Date: Tuesday, November 20, 2018 at 2:04 AM
> To: Matt Glasser
> Cc: Timothy Coalson ,
Left and right are registered.
Matt.
From: Reza Rajimehr mailto:rajim...@gmail.com>>
Date: Tuesday, November 20, 2018 at 2:04 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, hcp-users
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users]
Medial wall could have been excluded from a connectivity CIFTI file, not in
the file itself, but during an operation on the file using an option like
-exclude-medial-wall in the command. But I totally understand the rationale
for removing it in the first place.
On Tue, Nov 20, 2018 at 12:28 AM
Thanks Matt! Yes, having symmetric medial wall and having registered left
and right hemispheres would be helpful and important.
On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew wrote:
> We don’t want the non-greymatter medial wall in CIFTI; however, the medial
> wall may undergo revision in
We don’t want the non-greymatter medial wall in CIFTI; however, the medial wall
may undergo revision in the future and making it symmetric might be more
convenient, though this would might require rerunning the left/right
registration, which remains in all HCP Pipelines derived standard mesh
External interoperation with GIFTI and NIFTI data is the purpose of the
-cifti-separate command, it is much simpler than using
-cifti-export-dense-mapping.
A central goal of CIFTI was the exclusion of non-interesting locations from
the file (this becomes more important with dense connectivity
Thanks! The file that we looked into was an MSMSulc file. I guess that the
difference of 10 indices/vertices between left and right hemis exists for
an MSMAll file as well, but I haven’t checked it yet.
One comment: The medial wall has been left out in CIFTI files because the
medial wall is not
The left and right hemisphere are intended to be in register, though I
don't recall what effort was put into this in MSMAll (maybe only the
dedrifting to sulc). I believe the left and right hemisphere medial wall
masks were generated separately without trying to synchronize across
hemispheres,
We successfully used -cifti-export-dense-mapping to get the mapping from
cifti indices to surface vertices (all indices are zero-based).
wb_command -cifti-export-dense-mapping
100408_tfMRI_WM_level2_hp200_s2.dscalar.nii COLUMN -surface CORTEX_LEFT
leftcortex.txt
wb_command
The easiest to use (especially if your goal is to match other cifti files)
is generally -cifti-create-dense-from-template. It will even turn a 59k
surface-only cifti into a standard 91282 cifti (or vice versa, if you are
so inclined).
Yes, -cifti-export-dense-mapping will give you the cifti
See the various -cifti-create-* commands.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel:
Is there a command to convert LH (or RH) gifti file to hcp cifti file?
On Fri, Nov 16, 2018 at 10:55 PM Harms, Michael wrote:
>
>
> No, it is more complicated than that.
>
>
>
> I believe what you need is -cifti-export-dense-mapping
>
>
>
> Cheers,
>
> -MH
>
>
>
> --
>
> Michael Harms, Ph.D.
>
No, it is more complicated than that.
I believe what you need is -cifti-export-dense-mapping
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box
Thanks! Can I simply say that:
For left hemisphere:
vertex number in cifti = vertex number (up to 29706) in LH gifti
For right hemisphere:
vertex number in cifti = vertex number (up to 29706) in RH gifti + 29706
Or the mapping is more complicated than this?
On Fri, Nov 16, 2018 at 9:56 PM
That is correct, the medial wall is kept out. Usually when I want to do that I
split the CIFTI file into hemispheric GIFTI files, but perhaps there is a good
way to load in a specific mapping based on something we can output from
wb_command.
Matt.
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