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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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/[email protected]/msg03217.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 >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
