Re: [HCP-Users] activation region mask

[Glasser, Matthew]

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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