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/ > 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? > > > > > ------------------------------ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users