If you just want to look at them first, you can load them into wb_view. Depending on whether it is pdconn or dpconn (via a transpose), you will either get a dense map when you click a parcel, or a parcellated map when you click a vertex/voxel.
Tim On Mon, Jun 3, 2019 at 8:04 PM Joseph Orr <joseph....@tamu.edu> wrote: > I wanted to contrast the connectivity of the different parcels in order to > look for evidence of gradients in networks. I'll try it in matlab. > -- > Joseph M. Orr, Ph.D. > Assistant Professor > Department of Psychological and Brain Sciences > Texas A&M Institute for Neuroscience > Texas A&M University > College Station, TX > > > On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew <glass...@wustl.edu> > wrote: > >> Are you wanting to view the files? You could probably translate the file >> into a .dscalar.nii using matlab. >> >> >> >> Matt. >> >> >> >> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Joseph Orr < >> joseph....@tamu.edu> >> *Date: *Monday, June 3, 2019 at 7:55 PM >> *To: *HCP Users <hcp-users@humanconnectome.org> >> *Subject: *Re: [HCP-Users] pdconn analysis problems >> >> >> >> Thanks Tim, running cifti-transpose and separating on COLUMN solved both >> issues. Is there a way to separate the different parcels that make up a >> pdconn so that I can compare the connectivity maps between parcels? >> >> >> >> Thanks, >> >> Joe >> >> >> >> -- >> >> Joseph M. Orr, Ph.D. >> >> Assistant Professor >> >> Department of Psychological and Brain Sciences >> >> Texas A&M Institute for Neuroscience >> >> Texas A&M University >> >> College Station, TX >> >> >> >> >> >> On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson <tsc...@mst.edu> wrote: >> >> "Segmentation fault" is a computer term about invalid memory access, not >> related to the neuroscience term of segmentation. Due to using the wrong >> variable while copying map names, this command can crash when using ROW >> when the rows are longer than the columns. You can get around it by >> transposing and separating with COLUMN instead. This will be fixed in the >> next release. >> >> >> >> I don't know if this is also the reason palm was crashing. We could make >> a bleeding edge build available if you want to test it. >> >> >> >> Tim >> >> >> >> >> >> On Sat, Jun 1, 2019 at 2:17 PM Joseph Orr <joseph....@tamu.edu> wrote: >> >> Sure thing, here's a link to the file. Let me know if there are access >> problems and I can try another sharing via dropbox. >> >> *[image: Image removed by sender.] L-ctx_R-CB_crosscorr.pdconn.nii >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_a_tamu.edu_file_d_1W9n40sZgLNSn8ODIYf9xqBoAZ5b5C71E_view-3Fusp-3Ddrive-5Fweb&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0&s=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk&e=>* >> >> >> -- >> >> Joseph M. Orr, Ph.D. >> >> Assistant Professor >> >> Department of Psychological and Brain Sciences >> >> Texas A&M Institute for Neuroscience >> >> Texas A&M University >> >> College Station, TX >> >> >> >> >> >> On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >> It sounds like there might be both Workbench and PALM bugs here. Perhaps >> you could upload the data somewhere (off list if needed), so Tim and >> Anderson could take a look? >> >> >> >> Matt. >> >> >> >> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Joseph Orr < >> joseph....@tamu.edu> >> *Date: *Saturday, June 1, 2019 at 1:00 PM >> *To: *HCP Users <hcp-users@humanconnectome.org> >> *Subject: *[HCP-Users] pdconn analysis problems >> >> >> >> I have a pdconn input (cortical ptseries by subcortical dtseries) that >> I'd like to analyze with PALM, but I'm having some trouble. I only found >> one old post related to this, but the only suggestion was to use -transpose >> data flag in palm. When palm tries to read in the pdconn, I get an error >> "Undefined function or variable 'Y'". The command line output is below. I >> tried with the data transposed and not, but I get the same error. I tried >> to separate the pdconn to just the volume, but this yielded a segmentation >> error: ($ wb_command -cifti-separate input.pdconn.nii ROW -volume-all test >> >> /Applications/workbench/bin_macosx64/wb_command: line 14: 1248 >> Segmentation fault: 11 >> "$directory"/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command "$@" >> ). >> >> >> >> Are there any additional commands I can run on a pdconn to separate each >> parcel and have a series of dconn files? I'd be interested in doing this in >> order to compare the dense connectivity maps for different parcels. >> >> >> >> Thanks! >> >> Joe >> >> >> >> *Command line output for palm* >> >> Running PALM alpha115 using MATLAB 9.5.0.1067069 (R2018b) Update 4 with >> the following options: >> -i input.pdconn.nii >> -transposedata >> -o palm >> -d design.mat >> -t design.con >> -T >> Found FSL in /usr/local/fsl >> Found FreeSurfer in /Applications/freesurfer >> Found HCP Workbench executable in >> /Applications/workbench/bin_macosx64/wb_command >> Reading input 1/1: input.pdconn.nii >> Error using palm_ready >> (/Users/josephorr/Documents/MATLAB/palm-alpha115/palm_ready.m:141) >> Undefined function or variable 'Y' >> >> >> >> >> >> >> >> -- >> >> Joseph M. Orr, Ph.D. >> >> Assistant Professor >> >> Department of Psychological and Brain Sciences >> >> Texas A&M Institute for Neuroscience >> >> Texas A&M University >> >> College Station, TX >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70&m=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0&s=-sOhlQpS5zUxskE5tEKknxgLJgLb0cuMGQeOr9Krwok&e=> >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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