Hi Tim, Thanks for the reply. Yep, I was trying to use label-modify-keys on a cifiti file, so that explains it.
Cheers, Aaron On Tue, May 22, 2018 at 6:28 AM, Timothy Coalson <tsc...@mst.edu> wrote: > Oh, I have a guess as to what you encountered: the -label-modify-keys > command is only for gifti label files, not cifti, so it probably told you > something like "parse error on line 1". It looks like I didn't implement > equivalents for other formats, probably related to the fact that label > tables are separate per map in volume and cifti label files, but only one > for the whole file in gifti label files. > > Tim > > > On Mon, May 21, 2018 at 11:18 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> I think you must be using an older version of workbench, the recent 1.3.0 >> release appears to do those commands correctly. Do "wb_command -version" >> to check. I'll take a look at the -label-modify-keys command, can you be >> more specific about what it did? >> >> Note that Neurodebian has not yet updated workbench, we have a few things >> to work out with them. Hopefully it will be ready soon. >> >> Tim >> >> >> On Mon, May 21, 2018 at 10:33 AM, Aaron R <aaro...@gmail.com> wrote: >> >>> Never mind, I managed to figure it out. The command label-modify-keys >>> doesn't seem to work however, which makes fixing the key values a bit more >>> cumbersome. >>> >>> Cheers, >>> Aaron >>> >>> On Sun, May 20, 2018 at 12:21 AM, Aaron R <aaro...@gmail.com> wrote: >>> >>>> I've attempted to combine cortical and subcortical parcellations on a >>>> few occasions without any luck, I'm hoping someone here can help me out. >>>> >>>> #make some subcortical labels >>>> wb_command -cifti-create-label subcortical.dlabel.nii -volume >>>> Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz >>>> >>>> #combine with cortical >>>> wb_command -cifti-create-dense-from-template >>>> 91282_Greyordinates.dscalar.nii TEST.dlabel.nii -cifti >>>> glasser_cort.dlabel.nii -cifti subcortical.dlabel.nii >>>> >>>> ... seg fault >>>> >>>> #try -cifti-merge-dense >>>> wb_command -cifti-merge-dense COLUMN TEST.dlabel.nii -cifti >>>> glasser_cort.dlabel.nii -cifti subcortical.dlabel.nii >>>> >>>> #check >>>> wb_command -file-information TEST.dlabel.nii >>>> >>>> ... everything looks ok.. >>>> >>>> #try to use it, look at the output after running through task pipeline >>>> wb_command -file-information subject_TEST.pscalar.nii >>>> >>>> And parcellations are incorrectly merged, exactly like described here: >>>> https://www.mail-archive.com/hcp-users@humanconnectome.org/m >>>> sg03217.html >>>> >>>> I also apparently created a dlabel file another way, I don't remember >>>> how, but the parcellations were incorrectly merged as above. I extracted >>>> the labels to text, manually edited the key values in vi and reimported >>>> them.. it looked ok then (dlabel.nii), however the output (pscalar.nii) >>>> again was incorrectly merged as above. >>>> >>>> Can anyone tell me how to do this? >>>> >>>> Thank you, >>>> Aaron >>>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
