Hi Michael, Please see an example in this page: https://fsl.fmrib.ox.ac.uk/fsl /fslwiki/PALM/Examples
The Example 9 is for simple statistics on brainordinates (no spatial statistics) and Example 10 is for TFCE and cluster-level inference. Thanks to Tim Coalson for the help with the wb_command options. Hope this helps! All the best, Anderson On 15 September 2016 at 07:21, Anderson M. Winkler <[email protected]> wrote: > 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.hu >> manconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb >> 62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf9 >> 9IoNsmxWf1JolkKMmL6bXnYFSwg&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
