Hi Mahshid, Another approach might be for you to generate a 'foci' file based on the coordinates of your vertices of interest. Workbench supports foci files and projects them to the nearest surface vertices so that they stay 'glued' to the surface when viewed in different configurations.
Unfortunately, we don't yet have a wb_command option to generate foci files from your type of input data, though we will add it to the wb_command wish list. In the meantime, if this option appeals to you and you are impatient (need to move forward), it would be possible to do this by creating the foci in Caret5, then using wb_import to convert from caret5 to workbench format. If you decide to go down that road, it may be a bit laborious; we (Donna Dierker and/or Erin Reid) can probably help you out but it would be best to keep the gory details away from this list serve. David On Apr 7, 2014, at 3:03 PM, Timothy Coalson <[email protected]> wrote: > Yes, though it takes a bit of doing currently. -metric-reduce with INDEXMAX > gets you close to what you want, but you also need to mask out areas that are > zero in all maps. We recently worked out how to do this for our own purposes > with the currently available commands: > > -metric-reduce INDEXMAX on the multi-map file, I'll refer to this result as > "indices.func.gii" > -metric-reduce with SUM on the multi-map file, referred to as "sum.func.gii" > -metric-math 'x * (mask > 0)' with x being "indices.func.gii", and mask being > "sum.func.gii" > -metric-label-import on the result of the math command (to be able to assign > colors rather than using a metric palette) > > Tim > > > > On Mon, Apr 7, 2014 at 2:46 PM, Mahshid Najafi <[email protected]> wrote: > Thanks Tim, > Everything worked, except putting all in one map. Even though I used > overlap-logic CLOSEST, I could not make them as a gifti file with one map and > the output is a gifti file with the same number of maps as the number of > ROIs. Is it possible to somehow convert or merge all of maps in the gifti > file so they can be shown at the same time? > > Thanks > > > On Fri, Apr 4, 2014 at 4:58 PM, Timothy Coalson <[email protected]> wrote: > You could try using wb_command -surface-geodesic-rois, it will draw circular > ROIs around vertices, as separate maps in a metric file. If you want them > all in one map, the -overlap-logic option to that command, and the commands > -metric-reduce, -metric-math and -metric-label-import may come in handy. > > Tim > > > > On Fri, Apr 4, 2014 at 2:00 PM, Mahshid Najafi <[email protected]> wrote: > Thank you for your suggestions, The wb_command -cifti-seprate worked well. > > I have another question which is related to my question regarding uniofrmly > spaced ROIs. I have saved the index of vertices in a text file which are > distanced uniformly from each other and I know these are the vetices on which > cortex. Now I want to somehow visualize them in workbench. Do you have any > suggestion how to convert or use the text file of vertices to a format which > can be visualized by workbench? > > Thanks for your helps, > Mahshid > > > On Tue, Mar 25, 2014 at 1:51 PM, Mahshid Najafi <[email protected]> wrote: > Hi, > I have some problems in understanding the > rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii data. I used wb_command > -cifti-convert -to-gifti-ext rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii > rest_gifti to convert CIFTI to gifti and used gifti toolbox to load data in > the MATLAB. > Q1: The size of data is (91282,1200). I know 1200 is the time dimension, and > 91282 should be right and left hemisphere vertices + subcortical voxels, > right? If so, how can I understand if each column is which vertex or voxel of > the brain? i.e, I do not know in what order the data is saved > > Q2. How can I define uniformly distanced ROIs on the grayordinate data, which > includes specific number of vertices/voxels? > > Thanks very much, > Mahshid > > _______________________________________________ > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
