I should probably rephrase some of -cifti-label-import help.  When it says:

"The label list file must have lines of the following format:

      <value> <red> <green> <blue> <alpha>"

It means 2 lines per label: the first line is the label name, the second
line is the numeric stuff, where <key> is an integer that you will find in
the data file you are importing to label.

If you don't need to assign names to your labels, just specify '' as the
filename - a pair of quotes with nothing inside them (double quotes will
also work) - quoting from the help:

"You may specify the empty string ('' will work on linux/mac) for
<label-list-file>, which will be treated as if it is an empty file."

Then it will just assign names based on what value it found in the file
being imported:

"By default, it will set new label names with names of LABEL_# for any
values encountered that are not mentioned in the list file, specify
-discard-others to instead set these to the "unlabeled" key."

You do want these imported, rather than zeroed out, so you don't want to
use -discard-others.


On Tue, Sep 20, 2016 at 3:00 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> Thank you, I was using a bad input file. The command works now.
> for -cifti-label-import however, I am no sure how the label file is
> supposed to look. I get a malformed error:
> ERROR: label list file is malformed for entry #1: test 255 255 255 255
> I have 4 cortical and 1 subcortical ROIs which are colored differently on
> viewing, but the cifti file contains only 1 map.
> Ultimately I’d like to be able to identify and extract beta weights from
> each.
> Thank you,
> Michael
> On Sep 20, 2016, at 2:26 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> What does the input data look like?
> Peace,
> Matt.
> From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>
> Date: Tuesday, September 20, 2016 at 1:22 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>, Timothy Coalson <
> tsc...@mst.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
> OK, I tried this:
> wb_command -cifti-find-clusters FoodGo_HCP_mesh_TFCE_palm/
> FoodGo_results_merged_tfce_tstat_fwep.dscalar.nii 0 0 0 0 COLUMN
> FoodGo_results_merged_tfce_tstat_fwep_ROIs.dscalar.nii -left-surface
> HCP_S900_GroupAvg_v1/S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii
> -right-surface HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.
> surf.gii
> Where now I am using these 900 subject average files as templates. I
> though the -left-surface it was looking for was with the statistics run
> The output of this is null, however. Nothing shows up on wb_view and
> -file-information gives:
> Map   Minimum   Maximum    Mean   Sample Dev   % Positive   % Negative
> Inf/NaN   Map Name
>   1     0.000     0.000   0.000        0.000        0.000        0.000
>     0   #1
> Am I doing something wrong still?
> Thanks,
> Michael
> On Sep 20, 2016, at 1:59 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> Presumably you have some of these if you have gotten this far?
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