Let me expand a bit on wb_shortcuts -cifti-concatenate (which I incorrectly attributed to wb_command in my last email). The syntax looks like this:
wb_shortcuts -cifti-concatenate output.dscalar.nii input1.dscalar.nii input2.dscalar.nii input3.dscalar.nii This causes output.dscalar.nii to be written, and it will contain the data of input1.dscalar.nii, followed by input2.dscalar.nii, and input3.dscalar.nii. You can specify as many inputs as needed, subject to technical limitations such as maximum number of open file descriptors. Again though, you should not use this command on surface files (nor any other gifti files, nor volume files). There are -metric-concatenate (for .func.gii) and -volume-concatenate (for .nii.gz) commands for other file types, but there is intentionally no such command for surface files. Tim On Mon, Dec 19, 2016 at 7:17 PM, Timothy Coalson <tsc...@mst.edu> wrote: > Surface files cannot be concatenated. Is there something that instructs > you to do this (or seems to imply it)? If so, it should be corrected. > > For TFCE in PALM, what you probably want is group-average vertex areas, > and then it doesn't really matter what surfaces you use (as it only takes > the connectedness information from them). The average vertex areas are > meant to compensate for the loss of folding definition and therefore > surface area when averaging surface coordinates together. See here: > > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03820.html > > Side note: wb_command -cifti-concatenate works only on cifti files, and > surface files are not cifti files. See these links for explanation: > > http://www.humanconnectome.org/software/workbench- > command.php?function=-gifti-help > http://www.humanconnectome.org/software/workbench- > command.php?function=-cifti-help > > Tim > > > On Mon, Dec 19, 2016 at 6:55 PM, Durgerian, Sally <sal...@mcw.edu> wrote: > >> Dear HCP experts, >> I’m groping around in the dark about how to concatenate various filetypes >> of individual subject data in order to do a group analysis in PALM. >> Most of the examples seem to assume that I already know how to do that. >> Or maybe I’m not understanding this at an even higher level. >> >> Here’s what I’m trying to do: >> I have a group of subjects and a design matrix, and I want to use PALM to >> do joint inference. I was thinking I should use the files in each subject's >> MNINonLinear/fsaverage_LR32k/ directory, specifically: >> L and R.MyelinMap.32k_fs_LR.dscalar.nii, >> L and R.ArealDistortion_FS.32k_fs_LR.shape.gii and >> L and R.corrThickness.32k_fs_LR.shape.gii >> >> I want to do TFCE, so I also need to use each subject’s concatenated L >> and R.midthickness.32k_fs_LR.surf.gii (right?), and also the mean area >> files (L and R_area.func.gii) I created as shown in Example 10 of the PALM >> examples. >> I have somehow managed, probably in a really kludgey way, to get this >> working without TFCE, but I can’t figure out how to concatenate the surface >> files properly, or even whether I’m using the right files. >> >> Am I on the right track, and how do I concatenate the subject files for >> each of these data types so that their matrices all get read in the proper >> orientations? >> I would appreciate it if you would give the example as an entire command, >> rather than saying “use cifti-concatenate”, because I may be getting some >> part of the syntax wrong. And also, please let me know if I have not chosen >> the optimal group of input files for the task. >> Thanks so much, >> Sally >> >> Sally Durgerian >> Neurolab G2415 >> Medical College of Wisconsin >> 8701 W. Watertown Plank Rd. >> Milwaukee WI 53226 >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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
