Thank you very much. When I merge my cope files I was getting the same errors as before when I ran the following command:
palm -i TGNGcope1.dtseries.nii -transposedata -fdr -d $LevelThreeFEATDir/design.mat -t $LevelThreeFEATDir/design.con -T -ise When I removed the "-t $LevelThreeFEATDir/design.con" then palm appears to run smoothly, so the problem was coming from there. I thought that argument was necessary to indicate that this was a one-sample t-test, but I the .mat file is sufficient. By the way, are the materials for the course available somewhere now? I'd love to see them. I am also not familiar with palm_vestwrite, and I haven't been able to any documentation online. Thank you, Michael ________________________________ From: Burgess, Gregory <[email protected]> Sent: Tuesday, September 13, 2016 10:24:14 AM To: Michael F.W. Dreyfuss Cc: [email protected]; Anderson M. Winkler Subject: Re: [HCP-Users] PALM with cifti files Hi Michael, I assume that each cope map is viewable in Connectome Workbench... that is to say that each CIFTI cope has 91282 rows and 1 column. For the recent HCP Course, we suggested merging the individual subject copes into a dtseries with 91282 rows x S columns, where S was the number of subjects. # Start an empty variable to store the list of arguments: args="" # For each subject: for subj in $(cat list101.txt) ; do # Append the respective arguments to the list (below it’s all a single line): args="${args} -cifti ${PRACTICALS}/day3-tuesday/tfMRI/DATA/${subj}/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s2_level2_Glasser.feat/ParcellatedStats/cope11.feat/cope1.ptseries.nii -column 1" done # Run the wb_command to merge all into a single file: wb_command -cifti-merge Y.ptseries.nii ${args} Then set the merged CIFTI output as the single input file with the -i option. The .mat and .con can be written using palm_vestwrite, but I believe that PALM will work directly with the output of FSL's GLM GUI as well. Give that a try. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Neuroscience Phone: 314-362-7864<tel:314-362-7864> Email: [email protected]<mailto:[email protected]> On Sep 12, 2016, at 1:50 PM, Burgess, Gregory <[email protected]<mailto:[email protected]>> wrote: Hi Michael, I just want to verify that you are trying to use PALM for “higher-level” group analyses. PALM is not currently able to conduct “lower-level” timeseries analyses. You currently need to use the HCP task fMRI pipelines for that. If you are attempting group analyses, it might be helpful to know the error messages that you are receiving. Thanks, --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864 Email: [email protected]<mailto:[email protected]> On Sep 12, 2016, at 1:40 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: Do you have the latest version of PALM? Does it work if you convert the files to dscalar? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Michael F.W. Dreyfuss" <[email protected]<mailto:[email protected]>> Date: Monday, September 12, 2016 at 1:15 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] PALM with cifti files Hello, I am getting errors when I try to use palm with cifti files. Is there an option or options that I need to use with palm for it to read dtseries.nii files appropriately? Are there any examples of simple implementations of palm on cifti type fMRI data (task based especially)? Thanks you, Michael _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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=DQMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=VWfrJpUqjyIZTdfS8bV3UncsDU4Nb7PapN0IGXkgvco&s=6l8AoYfzyRyaw4SxkKpiADjH9zf4UQCquUab_lmLcIM&e=> 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. 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If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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=DQMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=VWfrJpUqjyIZTdfS8bV3UncsDU4Nb7PapN0IGXkgvco&s=6l8AoYfzyRyaw4SxkKpiADjH9zf4UQCquUab_lmLcIM&e=> ________________________________ 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. 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