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
