Structures are not labels, you need to use CORTEX_LEFT and CORTEX_RIGHT with -cifti-separate, that error says the structure you specified isn't a structure contained in the cifti file. However, it outputs gifti files, and if those don't work in your tractography program, you may need to do some additional conversion.
Also, if you want gifti label files from a cifti dlabel file, use -label instead of -metric with -cifti-separate. Tim On Thu, May 1, 2014 at 9:47 PM, Luo,Yishan <lys84...@hotmail.com> wrote: > > I am using dsistudio for fiber tracking. It doesn't accept gifti file. > > I tried -cifti-separte -metric, but it reports: ERROR: getSurfaceMap > called for nonexistant structure > > I used -cifti-label-import to create the dlabel file > my labellist is "OTHER > 1 255 0 0 100" > > So for -metric <structure> I use OTHER for structure. > > But happens for this error? > > Thanks very much for your help. > > Lisa > > > ------------------------------ > From: glass...@wusm.wustl.edu > To: lys84...@hotmail.com; tsc...@mst.edu > CC: do...@brainvis.wustl.edu; hcp-users@humanconnectome.org > > Subject: Re: [HCP-Users] activation region mask > Date: Wed, 30 Apr 2014 14:38:45 +0000 > > > What fiber tracking software are you using? probtrackx accepts GIFTI > labels on the surface. wb_command -cifti-separate -volume-all only > separates out the subcortical data. To get the surface data you need to > specify the -metric outputs. > > Peace, > > Matt. > > From: <Luo>, Yishan <lys84...@hotmail.com> > Date: Wednesday, April 30, 2014 at 3:15 AM > To: Matt Glasser <glass...@wusm.wustl.edu>, Timothy Coalson < > tsc...@mst.edu> > Cc: Donna Dierker <do...@brainvis.wustl.edu>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: RE: [HCP-Users] activation region mask > > Thanks all for your answers. The problem was solved by > using -cifti-label-import. > > Sorry for bothering. Here I have another question: > > I have a label file *.dlabel.nii (created by thresholding the > *tfMRI_MOTOR_level2_hp200_s4.dscalar file, in my previous question) > > I print the information of this file to a txt file, and find there are > 14326 nonzero labels. > I'd like to change this file into a normal nifti file in mni space, so > that I can use it as a roi region for fiber tracking, > I use the command "-cifti-separate -volume-all " > and change it into a *.nii file, but when I read the file, I find there > are only 3256 labels. > > I dont know why some labels are discarded. > > > > Best Regards, > Lisa > > > ------------------------------ > From: glass...@wusm.wustl.edu > To: tsc...@mst.edu > CC: do...@brainvis.wustl.edu; lys84...@hotmail.com; > hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] activation region mask > Date: Tue, 29 Apr 2014 18:20:19 +0000 > > That command needs a -cifti-roi flag added to it for it to be usable in > this case I think (and I think it should be added). > > Matt. > > From: Timothy Coalson <tsc...@mst.edu> > Date: Tuesday, April 29, 2014 at 1:19 PM > To: Matt Glasser <glass...@wusm.wustl.edu> > Cc: Donna Dierker <do...@brainvis.wustl.edu>, "Luo,Yishan" < > lys84...@hotmail.com>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] activation region mask > > Sorry, didn't get the URL right: > http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-average-dense-roi > > Tim > > > > On Tue, Apr 29, 2014 at 1:18 PM, Timothy Coalson <tsc...@mst.edu> wrote: > > If you have only one ROI, you could also look at > the -cifti-average-dense-roi command: > http://www.humanconnectome.org/software/workbench-command.php > > Tim > > > > On Tue, Apr 29, 2014 at 10:11 AM, Glasser, Matthew < > glass...@wusm.wustl.edu> wrote: > > To convert the output of -cifti-math to a label file, use wb_command > -cifti-label-import. You can use wb_command -cifti-merge to extract > frames, though it is not as convenient as something like fslroi would be > as you have to specify each frame. > > Peace, > > Matt. > > On 4/29/14, 8:19 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: > > >Hi Lisa, > > > >While there is a -volume flag (e.g., for subcortical structures), it is > >not mandatory. This command works for me: > > > >wb_command -cifti-create-label $OUTPUT_DLABEL_1 \ > > -left-label $INPUT_LABEL_LH -right-label $INPUT_LABEL_RH > > > >I'm sorry I don't know how to extract the frames. > > > >Donna > > > > > >On Apr 29, 2014, at 2:48 AM, "Luo,Yishan" <lys84...@hotmail.com> wrote: > > > >> Dear all, > >> > >> I would like to do the following things with task fMRI. > >> > >> I threshold the file > >>HCP_Q1-2_R120_tfMRI_ALLTASKS_level3_hp200_s4.dscalar.nii to get the > >>activation region > >> using -cifti-math "x>5" > >> > >> I want to extract the average timeseries from the roi region. > >> But it seems that -cifti-parcellate requires a label file as input. And > >>-cifti-create-label requires a volume file as input to create a label. > >> But my output from -cifti-math is in cifti format, it is neither a > >>volume nor a label. > >> > >> How can I do to transform it? > >> > >> Another question is how can I extract several frames from > >>"tfMRI_MOTOR_LR_Atlas.dtseries.nii" file, such as from frame 10 to 20? > >> > >> > >> Thanks a lot! > >> > >> Best Regards, > >> Lisa > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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 > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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