Hi Michael, Thanks for including the full error message -- this is helpful and suggests that the surface file is likely not in the correct size. Could you please also post the full command line that lead to this error. Also, please do upload the images via the OxFile link you should have received yesterday. Thanks.
All the best, Anderson On 14 September 2016 at 04:38, Michael F.W. Dreyfuss < [email protected]> wrote: > I was mistaken; the command gives this error when I use the option -T to > run TFCE, and palm runs smoothly when I do not use that option. Once > again the error is: > > > Building null distribution. > 0.01% [Design 1/1, Contrast 1/1, Shuffling 1/10000, Modality 1/1] > Saving file: palm_dat_tstat > Index exceeds matrix dimensions. > > Error in palm_tfce (line 77) > elseif plm.Yisvtx(y) || plm.Yisfac(y), > > Error in palm_core (line 1680) > Gtfce{y}{m}{c} = > tfcefunc(G{y}{m}{c},y,opts,plm); > > Error in palm (line 81) > palm_core(varargin{:}); > > Would you have any suggestion for how I can run TFCE with palm here? Or is > anything else recommended for identifying clusters of activation? > > > Thank you, > > Michael > ------------------------------ > *From:* Michael F.W. Dreyfuss > *Sent:* Tuesday, September 13, 2016 12:25:03 PM > *To:* Burgess, Gregory > > *Cc:* [email protected]; Anderson M. Winkler > *Subject:* Re: [HCP-Users] PALM with cifti files > > > 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 ${PRACTICALS}/day3-tuesday/tfM > RI/DATA/${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 > Email: [email protected] > > On Sep 12, 2016, at 1:50 PM, Burgess, Gregory <[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] > > On Sep 12, 2016, at 1:40 PM, Glasser, Matthew <[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]> on behalf of "Michael F.W. > Dreyfuss" <[email protected]> > > Date: Monday, September 12, 2016 at 1:15 PM > > To: "[email protected]" <[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] > > 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. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > > HCP-Users mailing list > > [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. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > [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. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
