Also, if you literally want spatial gradient magnitude, you can run -cifti-gradient on the correct dimension of the pdconn (or dpconn) file.
Tim On Mon, Jun 3, 2019 at 8:14 PM Timothy Coalson <tsc...@mst.edu> wrote: > 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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