Hi Michael, TFCE needs to be run separately for the surface-based and for the volume-based parts of the CIFTI file. This means that the input file has to be separated using wb_command, then PALM be executed, then the results need to be corrected via Bonferroni or Šidák. I will add hopefully today still a section in the documentation with the steps and update here.
Also, although it's unrelated to this error, Donna is right: the extension for the -t option wasn't supplied correctly. All the best, Anderson On 15 September 2016 at 06:22, Michael F.W. Dreyfuss < [email protected]> wrote: > Thank you, > > > The $ContrastName is the argument of the -o option, so it is just the name > designated for the output. There are no csv files unless you mean the .mat > and .con files which are the arguments of -d and -t respectively for the > design files and contrast files. Since it is a group average, it actually > runs without the contrast file as well. > > > Again, this whole command runs fine and gives reasonable output with the > -fdr flag instead of -T, but I would like to be able to run TFCE here. Has > the -T option been used with palm on cifti data successfully? Maybe it is > not meant is only for use on volumetric data? > > > Thanks a lot, > > Michael > ------------------------------ > *From:* Dierker, Donna <[email protected]> > *Sent:* Wednesday, September 14, 2016 11:09:04 PM > *To:* Michael F.W. Dreyfuss > *Cc:* [email protected] > *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data > > Michael, if $ContrastName is a csv file, make sure its extension is csv. > I’ve gotten errors like that before when I named it .con. > > > > > > > On Sep 14, 2016, at 11:29 AM, Michael F.W. Dreyfuss < > [email protected]> wrote: > > > > > > Hello, I am trying to run palm on cifti data with TFCE to find mean > activation across a group. When I use the -T flag, the program crashed with > the error: > > > > > > Command: > > > palm -i ${ContrastName}.dtseries.nii -transposedata -d > $LevelThreeFEATDir/design.mat -o $ContrastName -t > /tmp/CtxFGNG/CtxFGNG_Level3_Analysis/desion -T -ise > > > > > > Error: > > > 0.01% [Design 1/1, Contrast 1/1, Shuffling 1/10000, Modality 1/1] > > > Saving file: FoodNogo_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{:}); > > > > > > > > > Alternatively, if I use the same command, but replace -T with -fdr, the > program runs smoothly, so I do not think the problem is with my design > files or data unless they need to be generated in a special way for TFCE > using palm. Are there any recommendation or previous examples of how I can > use TFCE on cifti data using palm? > > > > > > Any help on this is very appreciated. > > > > > > Thank you, > > > Michael > > > _______________________________________________ > > > HCP-Users mailing list > > > [email protected] > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ& > c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_ > z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=r90wcW3hZmEtN5Op3za0BAuX5uqah- > NHkwg8a_Q7XII&s=3G_GSd6Y2Hl4j0R9IXFYn7JG7IJ5qEetuM339dG1HHg&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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
