Re: [HCP-Users] activation region mask

[Glasser, Matthew]

There is a way to make probtrackx produce a deterministic like output, you can ask on the FSL list how to do that. Peace, Matt. From: <Luo>, Yishan <lys84...@hotmail.com> Date: Wednesday, May 7, 2014 at 4:39 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 very much for your suggestion. I found that FSL's probtrackx is probabilistic fiber tracking. And it is really slow, even with parallel computing. What I need is only deterministic fiber tracking. But I found most of deterministic fiber tracking tools don't accept gifti file as seed region. So I am sorry still confused with the question, how to transfer a label.gii file into a volumetric *.nii file for easy use. Thanks a lot! Lisa From: glass...@wusm.wustl.edu To: tsc...@mst.edu; lys84...@hotmail.com CC: do...@brainvis.wustl.edu; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] activation region mask Date: Fri, 2 May 2014 05:06:35 +0000 I would recommend FSL’s probtrackx for tractography and you can visualize the results in Connectome Workbench.  I’ve never heard of dsistudio, so I don’t know how to help you use it.  We don’t provide DSI data, but rather 3-shell HARDI data.   Peace, Matt. From: Timothy Coalson <tsc...@mst.edu> Date: Thursday, May 1, 2014 at 10:30 PM To: "Luo,Yishan" <lys84...@hotmail.com> Cc: Matt Glasser <glass...@wusm.wustl.edu>, Donna Dierker <do...@brainvis.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] activation region mask The command is not asking you for a label name, it is asking you which surface you want, and the current options with our data are left cortex and right cortex.  You asked it to find the "OTHER" surface, which doesn't exist ("nonexistant structure"). Our data has left and right cortex surface data in it to begin with, thresholding and importing to label doesn't change that.  The label name you used in -cifti-label-import is irrelevant to this command.  Use CORTEX_LEFT and CORTEX_RIGHT. Tim On Thu, May 1, 2014 at 10:09 PM, Luo,Yishan <lys84...@hotmail.com> wrote: I tried -label option and OTHER as my structure name,  it gives me the same error message. I am wondering is there any wrong with my labellist file? because i specify my label to be named OTHER,  there is nor CORTEX_LEFT CORTEX_RIGHT in my label file. Lisa Date: Thu, 1 May 2014 22:00:41 -0500 Subject: Re: [HCP-Users] activation region mask From: tsc...@mst.edu To: lys84...@hotmail.com CC: glass...@wusm.wustl.edu; do...@brainvis.wustl.edu; hcp-users@humanconnectome.org 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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