You can count the number of vertices in an ROI metric file with wb_command -metric-stats using SUM (the ROI should be the input, you don't need -roi).
Tim On Tue, Apr 17, 2018 at 7:31 AM, Xinyang Liu <[email protected]> wrote: > Dear Matt, dear Tim, > > Lots of thanks! I have a better understanding now owing to your detailed > explanation. :) > By the way, is there any command in the workbench to count the vertex > number on single surface ROI? > > Best regards, > Xinyang > > > At 2018-04-17 08:11:23, "Glasser, Matthew" <[email protected]> wrote: > > It is better to have the termination surface outside the counting surface > (e.g. count on white, terminate on pial). I do not remember if they can be > the same surface or not, so you would need to ask this on the FSL list. > > Peace, > > Matt. > > From: Timothy Coalson <[email protected]> > Date: Monday, April 16, 2018 at 4:10 PM > To: Xinyang Liu <[email protected]> > Cc: HCP 讨论组 <[email protected]>, Matt Glasser < > [email protected]> > Subject: Re: [HCP-Users] using surfaces as termination masks > > Inline replies. > > Tim > > On Sun, Apr 15, 2018 at 9:42 AM, Xinyang Liu <[email protected]> > wrote: > >> Dear Matt, dear Tim, >> >> Very grateful for both of your kind replies. :) >> >> Here are some further questions based on your feedbacks. >> >> 1. For the ROI of neocortex (atlasroi.shape.gii), does it mean this >> shape file includes pial, midthickness and white surfaces? I previously >> thought the .shape.gii file provides cortical shape information, like >> curvature. But then I found the value of each atlasroi vertex is 1. Is >> it just an atlas map? Why was it chosen to set the value of L/R white.asc >> in surf2surf for brain surfaces? How do we usually give the --values in >> surf2surf? >> > > .shape.gii is a file extension, it does not tell you what is in the file. > It is actually the same file format as .func.gii, and we are not entirely > consistent about when we choose to use each one. "atlasroi.shape.gii" is > just a binary roi, as "atlasroi" is intended to imply - it has values of 1 > on vertices that get used in our standard cifti space, and 0 on vertices > that don't get used. There are no coordinates or topology in it, no white, > no pial, no midthickness - it is not a .surf.gii file, and we don't use the > "combined data and coordinates" type files that other software does > (unfortunately, probtrackx requires such "combined" files, adding to your > confusion). In workbench, surfaces are always loaded from a different file > than the data to display on them. > > >> 2. For the CIFTI and GIFTI matrices, I didn't intend to get the value of >> each element, but preferred to know what kind of data is stored, which >> might be shown by the name of each column, or data can be recognized as >> coordinates. I am wondering how to check this. >> > > They can store any type of measure. You can get the names of the maps, if > they have been named at all, by using "wb_command -file-information > -only-map-names <file>". Cifti files only store data values, and do not > additionally contain surface coordinates or topology. You have to load > surfaces separately from the cifti file. > > >> 3. I could not understand well that the cortex ROI would allow >> connections to pass through the medial wall. Because when looking at the >> surface outlines of "L/R.white.32k_fs_LR.surf.gii", it seems that the >> left and white surfaces are closed regions (please see the figure >> attached). Then how do connections pass through the middle surfaces? >> > > The atlasroi.shape.gii has values of 0 on the vertices that cut through > the corpus callosum - if you generate the files correctly, the tractography > software will see these values of 0 and know not to terminate a streamline > that hits the surface where the value is 0, and continue until it hits a > vertex with a value of 1. You will need to specify the files for both > hemispheres to the tractography command, I assume. > > >> 4. If we acquire seed ROIs from the midthickness surface, does it mean >> that the termination surface masks can only come from the pial surface >> then? Because the white surface is in the inner layer and therefore would >> stop the streamlines coming from the mid-surface to go inside the brain. Is >> my understanding correct? >> > > I don't understand this question. I don't know if it is even possible to > specify multiple stopping surfaces for one hemisphere in probtrackx. If it > were, and you used the white surface as one of them, then it should stop > all streamlines before they reach midthickness or pial (unless you did > something wrong). I think the general guidance is to use the white matter > surface, as fiber directions become less reliable in gray matter. > > >> Look forward to your further guidance. Many thanks! >> >> Best regards, >> Xinyang >> >> >> >> At 2018-04-14 05:42:36, "Timothy Coalson" <[email protected]> wrote: >> >> Inline comment. >> >> Tim >> >> On Thu, Apr 12, 2018 at 11:01 PM, Xinyang Liu <[email protected]> >> wrote: >> >>> >>> 2. How to look at the CIFTI and GIFTI files as matrices? I haven't found >>> a proper way to look at the information inside as rows and columns. >>> >> >> Gifti files, and dense cifti files, have too many elements to be properly >> viewed as a matrix, and the vertices that are adjacent in the file data >> don't make much sense spatially. If you want a matrix display, you should >> use a parcellated cifti file (which can be made from a dense cifti file >> with wb_command -cifti-parcellate). >> >> Tim >> >> >> 1. That is the ROI of neocortex (excluding the medial wall). The medial >> wall is the non-cortical tissue that connects the two hemispheres (e.g. >> corpus callosum, diencephalon). All of the surface meshes are usable if >> they are the same kind of mesh (i.e. native, 32k, 164k). >> >> 2. You can convert them to dconn files with wb_command >> -probtrackx-dot-convert. >> >> 3. The cortex ROI will allow connections to pass through the medial >> wall. You can include multiple surface and volume ROIs in probtrackx. >> >> Peace, >> >> Matt. >> >> >> >> >> >> >> >> >> > > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
