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
"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
On Tue, Sep 20, 2016 at 3:00 PM, Michael F.W. Dreyfuss <
> 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
> Thank you,
> On Sep 20, 2016, at 2:26 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> What does the input data look like?
> 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>, "email@example.com" <
> 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
> -right-surface HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.
> 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?
> 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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