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<mailto: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<mailto: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 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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Joseph Orr <joseph....@tamu.edu<mailto:joseph....@tamu.edu>> Date: Saturday, June 1, 2019 at 1:00 PM To: HCP Users <hcp-users@humanconnectome.org<mailto: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<mailto: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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