Re: [HCP-Users] pdconn analysis problems
Got it, thanks! -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 8:14 PM Timothy Coalson 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 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 Institute for Neuroscience >> Texas A University >> College Station, TX >> >> >> On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew >> wrote: >> >>> Are you wanting to view the files? You could probably translate the >>> file into a .dscalar.nii using matlab. >>> >>> >>> >>> Matt. >>> >>> >>> >>> *From: * on behalf of Joseph Orr >>> >>> *Date: *Monday, June 3, 2019 at 7:55 PM >>> *To: *HCP Users >>> *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 Institute for Neuroscience >>> >>> Texas A University >>> >>> College Station, TX >>> >>> >>> >>> >>> >>> On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=>* >>> >>> >>> -- >>> >>> Joseph M. Orr, Ph.D. >>> >>> Assistant Professor >>> >>> Department of Psychological and Brain Sciences >>> >>> Texas A Institute for Neuroscience >>> >>> Texas A University >>> >>> College Station, TX >>> >>> >>> >>> >>> >>> On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew >>> 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: * on behalf of Joseph Orr >>> >>> *Date: *Saturday, June 1, 2019 at 1:00 PM >>> *To: *HCP Users >>> *Subject: *[HCP-Users] pdconn analysis problems >>> >>> >>> >>> I have a pdconn input (cortical ptseries by subcortical dtseries) th
Re: [HCP-Users] pdconn analysis problems
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 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 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 Institute for Neuroscience >> Texas A University >> College Station, TX >> >> >> On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew >> wrote: >> >>> Are you wanting to view the files? You could probably translate the >>> file into a .dscalar.nii using matlab. >>> >>> >>> >>> Matt. >>> >>> >>> >>> *From: * on behalf of Joseph Orr >>> >>> *Date: *Monday, June 3, 2019 at 7:55 PM >>> *To: *HCP Users >>> *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 Institute for Neuroscience >>> >>> Texas A University >>> >>> College Station, TX >>> >>> >>> >>> >>> >>> On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=>* >>> >>> >>> -- >>> >>> Joseph M. Orr, Ph.D. >>> >>> Assistant Professor >>> >>> Department of Psychological and Brain Sciences >>> >>> Texas A Institute for Neuroscience >>> >>> Texas A University >>> >>> College Station, TX >>> >>> >>> >>> >>> >>> On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew >>> 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: * on behalf of Joseph Orr >>> >>> *Date: *Saturday, June 1, 2019 at 1:00 PM >>> *To: *HCP Users >>> *Subject: *[HCP-Users] pdconn analysis problems >>> >>> >>> >>> I have a pdconn input (cortical ptseries by subcortical dtseries) that >>> I'd like to ana
Re: [HCP-Users] pdconn analysis problems
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 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 Institute for Neuroscience > Texas A University > College Station, TX > > > On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew > wrote: > >> Are you wanting to view the files? You could probably translate the file >> into a .dscalar.nii using matlab. >> >> >> >> Matt. >> >> >> >> *From: * on behalf of Joseph Orr < >> joseph....@tamu.edu> >> *Date: *Monday, June 3, 2019 at 7:55 PM >> *To: *HCP Users >> *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 Institute for Neuroscience >> >> Texas A University >> >> College Station, TX >> >> >> >> >> >> On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=>* >> >> >> -- >> >> Joseph M. Orr, Ph.D. >> >> Assistant Professor >> >> Department of Psychological and Brain Sciences >> >> Texas A Institute for Neuroscience >> >> Texas A University >> >> College Station, TX >> >> >> >> >> >> On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew >> 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: * on behalf of Joseph Orr < >> joseph@tamu.edu> >> *Date: *Saturday, June 1, 2019 at 1:00 PM >> *To: *HCP Users >> *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"/../macosx
Re: [HCP-Users] pdconn analysis problems
You don't need matlab for that, -cifti-change-mapping will let you reset a dimension to scalars. Depending on the input file, you may also need a -cifti-transpose to get a dscalar. Tim On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew wrote: > Are you wanting to view the files? You could probably translate the file > into a .dscalar.nii using matlab. > > > > Matt. > > > > *From: * on behalf of Joseph Orr < > joseph@tamu.edu> > *Date: *Monday, June 3, 2019 at 7:55 PM > *To: *HCP Users > *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 Institute for Neuroscience > > Texas A University > > College Station, TX > > > > > > On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=>* > > > -- > > Joseph M. Orr, Ph.D. > > Assistant Professor > > Department of Psychological and Brain Sciences > > Texas A Institute for Neuroscience > > Texas A University > > College Station, TX > > > > > > On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew > 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: * on behalf of Joseph Orr < > joseph@tamu.edu> > *Date: *Saturday, June 1, 2019 at 1:00 PM > *To: *HCP Users > *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' > > &g
Re: [HCP-Users] pdconn analysis problems
Each row or column (the shorter dimension) will be a dense map for connectivity to a parcel. Matt. From: Joseph Orr Date: Monday, June 3, 2019 at 8:03 PM To: "Glasser, Matthew" Cc: HCP Users Subject: Re: [HCP-Users] pdconn analysis problems 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 Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew mailto: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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Joseph Orr mailto:joseph@tamu.edu>> Date: Monday, June 3, 2019 at 7:55 PM To: HCP Users mailto: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 Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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. Error! Filename not specified. 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=> -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College Station, TX On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew 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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Joseph Orr mailto:joseph@tamu.edu>> Date: Saturday, June 1, 2019 at 1:00 PM To: HCP Users 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 Depa
Re: [HCP-Users] pdconn analysis problems
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 Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew wrote: > Are you wanting to view the files? You could probably translate the file > into a .dscalar.nii using matlab. > > > > Matt. > > > > *From: * on behalf of Joseph Orr < > joseph@tamu.edu> > *Date: *Monday, June 3, 2019 at 7:55 PM > *To: *HCP Users > *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 Institute for Neuroscience > > Texas A University > > College Station, TX > > > > > > On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=>* > > > -- > > Joseph M. Orr, Ph.D. > > Assistant Professor > > Department of Psychological and Brain Sciences > > Texas A Institute for Neuroscience > > Texas A University > > College Station, TX > > > > > > On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew > 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: * on behalf of Joseph Orr < > joseph@tamu.edu> > *Date: *Saturday, June 1, 2019 at 1:00 PM > *To: *HCP Users > *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 pa
Re: [HCP-Users] pdconn analysis problems
Are you wanting to view the files? You could probably translate the file into a .dscalar.nii using matlab. Matt. From: on behalf of Joseph Orr Date: Monday, June 3, 2019 at 7:55 PM To: HCP Users 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 Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=> -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College Station, TX On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew 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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Joseph Orr mailto:joseph@tamu.edu>> Date: Saturday, June 1, 2019 at 1:00 PM To: HCP Users 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 Institute for Neuroscience Texas A 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=-sOhlQpS5zUxskE5tEKknxgLJgLb0cuMGQeOr9Krwok=> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any
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 Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 5:14 PM Timothy Coalson 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 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. >> 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=DwMFaQ=ODFT-G5SujMiGrKuoJJjVg=ZKy1VO33u0kvO-PqY1gpb9Ld-AGhtT8c9PAcpsEyp70=dtQbE_Obfv7WQhtS5EGqWgePsIaI6hU895cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=> >> >> -- >> Joseph M. Orr, Ph.D. >> Assistant Professor >> Department of Psychological and Brain Sciences >> Texas A Institute for Neuroscience >> Texas A University >> College Station, TX >> >> >> On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew >> 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: * on behalf of Joseph Orr >>> >>> *Date: *Saturday, June 1, 2019 at 1:00 PM >>> *To: *HCP Users >>> *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 Institute for Neuroscience >>> >>> Tex
Re: [HCP-Users] pdconn analysis problems
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: on behalf of Joseph Orr Date: Saturday, June 1, 2019 at 1:00 PM To: HCP Users 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 Institute for Neuroscience Texas A University College Station, TX ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 Institute for Neuroscience Texas A University College Station, TX ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
