I should read the help info a little closer myself - I meant "<value>"
where I said "<key>" - perhaps "<key>" would be clearer in the help,
though...
Tim
On Tue, Sep 20, 2016 at 3:14 PM, Timothy Coalson <tsc...@mst.edu> wrote:
> I should probably rephrase some of -cifti-label-import help. When it says:
>
> "The label list file must have lines of the following format:
>
> <labelname>
> <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.
>
> Tim
>
>
>
> 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/Food
>> Go_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.mi
>> dthickness_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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