wb_command -cifti-help has a cheat sheet (and other useful explanation):
...
The common types of cifti files and the mapping types they use are:
dconn: ROW is dense, COLUMN is dense
dscalar: ROW is scalars, COLUMN is dense
dtseries: ROW is series, COLUMN is dense
...
"dense" is the mapping type that represents vertices and voxels, is the one
you need to modify. If you want to do it to the dconns, then you will need
to do it twice, because both dimensions are dense.
You can look through the hcp-users history here:
https://www.mail-archive.com/hcp-users@humanconnectome.org/
Tim
On Wed, Nov 28, 2018 at 8:44 PM Kenley, Jeanette <jkken...@wustl.edu> wrote:
> Thank you Tim and Matt for all the information.
>
>
> I currently am not using the HCP and unfortunately do not have the time to
> reprocess the data.
>
>
> I greatly appreciate the detailed explanation of the metric files and the
> difference between that and the label files. I am very new to surfaces and
> so everything is helpful!
>
>
> Just a couple more questions please.
>
> How do I know whether I want to use the 'COLUMN' or 'ROW' option?
>
> Is there a message board that I can look through other previously asked
> questions for future help?
>
>
> Thanks again,
>
> Jeanette
>
>
> ------------------------------
> *From:* Glasser, Matthew
> *Sent:* Wednesday, November 28, 2018 6:47 PM
> *To:* NEUROSCIENCE tim; Kenley, Jeanette
> *Cc:* hcp-users; Kaplan, Sydney
> *Subject:* Re: [HCP-Users] average dconn from individual dconns
>
> To be more specific: In the HCP we use a technique called MIGP to make
> group fMRI data and generate dense connectomes from that. Concatenated
> dense timeseries get very large when you have a lot of subjects and
> timepoints.
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy
> Coalson <tsc...@mst.edu>
> Date: Wednesday, November 28, 2018 at 2:54 PM
> To: "Kenley, Jeanette" <jkken...@wustl.edu>
> Cc: hcp-users <hcp-users@humanconnectome.org>, "Kaplan, Sydney" <
> sydney.kap...@wustl.edu>
> Subject: Re: [HCP-Users] average dconn from individual dconns
>
> The HCP pipelines deliberately resample the subcortical data in such a way
> that the subcortical voxels used in each subject are the same, this is how
> we handle the problem you are having.
>
> If you concatenate your timeseries across subjects before correlation, you
> don't need to generate a dconn for every subject, so this strategy uses
> less disk space (but you have to be careful about normalization before
> concatenation).
>
> Label files are not ROI files, though they might work in this case (you
> could instead use the .shape.gii files here:
> https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates).
> An ROI file is supposed to be a metric file (.func.gii, .shape.gii) of just
> 1's and 0's (the actual logic used is "greater than zero"). Label files
> can be used as metric files, the warning is just to let you know that you
> did something unusual. I'd need to see the actual error message to comment
> on it.
>
> If you don't want to go back to the timeseries (or reprocess with the HCP
> pipelines), -cifti-restrict-dense-map may be the simplest solution.
>
> Tim
>
>
> On Wed, Nov 28, 2018 at 2:00 PM Kenley, Jeanette <jkken...@wustl.edu>
> wrote:
>
> I am still new to the wb_command suite and trying to understand how to
> best use them.
>
>
> I have created an individual cifti (dconn.nii) for each of my subjects in
> 32kfslr and would like to make an average.
>
> I would like to use
>
> wb_command -cifti-average output.dconn.nii -cifti subject1.dconn.nii -cift
> subject2.dconn.nii . . .-cifti subjectN.dconn.nii
>
>
> But this results in a dimension mismatch since the sub cortical portions
> of the individual subjects are different.
>
>
> Is there a way to only grab the surface data from each of the individual
> dconns so I do not get the dimension error.
>
> I tried using
>
> wb_command -cifti-restrict-dense-map subjectN.dconn.nii 'ROW/COLUMN'
> subjectN_output.dconn.nii -left-roi $left -right-roi $right
>
>
> where the left and right rois are:
>
> subjectN.L.aparc.32k_fs_LR.label.gii
>
> subjectN.R.aparc.32k_fs_LR.label.gii
>
>
> but since I am newer to the wb_commands, I am not sure what each of the
> inputs should be or if this is the correct command.
>
>
> This also resulted in an error.
> WARNING: Metric File: subjectN.L.aparc.32k_fs_LR.label.gii contains data
> array with NIFTI_INTENT_LABEL !!!
>
> WARNING: Metric File: subjectN.R.aparc.32k_fs_LR.label.gii contains data
> array with NIFTI_INTENT_LABEL !!!
>
> As well as an error when I tried to use the file saying something about
> fields not being the same size.
>
>
> Or is there a way to generate the surface dconns via command line without
> the subcortical information so I don't get the dimension mismatch error
> when I try to make an average?
>
>
> Any help is greatly appreciated. And specific example file names are also
> very much appreciated.
>
>
> Thanks!
>
>
> ------------------------------
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