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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