Dear Darren,
Assuming that you are using PALM alpha112 with Octave on Ubuntu(?), I
think this will be fixed if you use the latest version of PALM from GitHub:
https://github.com/andersonwinkler/PALM/archive/master.zip
and recompile the MEX files.
Best regards,
Guillaume.
On 24/01/2019 00:34, Darren Campbell wrote:
> Hi
> Earlier I successfully conducted a permutation test on a subset of the HCP data (with the help of you guys). Now I am attempting to conducted the TFCE analysis version.
> I am following the Exploring the Human Connectome - Thursday, June 28, 2018 Practical 11: Task fMRI Analyses.
> Part 4 (Optional): Group analyses using PALM on dense maps (with TFCE)
> 4) Run the permutation test, now also with TFCE.
>
> After following the preliminary dataset preparation steps, I run the following palm command:
>
> palm -i ./HCP_subjects/Y_subcortical.nii -d ./HCP_subjects/Progs/Design.mat -t ./HCP_subjects/Progs/DesignGrpContr.con -o dense_subcortical_Results -n 1000 -corrcon -logp -accel tail -nouncorrected -T
>
>
> Feedback: / Errors
>
> Found FSL in /usr/local/fsl
> Found FreeSurfer in /usr/local/freesurfer
> Found HCP Workbench executable in /home/brain/workbench/bin_linux64/wb_command
> Reading input 1/1: ./HCP_subjects/Y_subcortical.nii
> warning: spm_existfile is not compiled for your platform.
> Reading design matrix and contrasts.
> warning: You chose to correct over contrasts, or run NPC
> between contrasts, but with the design(s) and,
> contrasts given it is not possible to run
> synchronised permutations without ignoring repeated
> elements in the design matrix (or matrices). To
> solve this, adding the option "-cmcx" automatically.
> Elapsed time parsing inputs: ~ 18.8976 seconds.
> Number of possible permutations is exp(810.477) = 190!.
> Generating 1000 shufflings (permutations only).
> Building null distribution.
> 0.0333% [Shuffling 1/1000, Design 1/1, Contrast 1/3, Modality 1/1]
> Saving file: dense_subcortical_Results_vox_tstat_c1
> Error using subsasgn>subfun ([log in to unmask]:164)
> mat2file: Can not yet write logical data.
>
> Error in subsasgn ([log in to unmask]:85->subsasgn>subfun)
> Error in subsasgn>fun ([log in to unmask]:74->subsasgn)
> Error in subsasgn ([log in to unmask]:20->subsasgn>fun)
> Error in palm_miscwrite (/home/brain/palm-alpha112/palm_miscwrite.m:102->subsasgn)
> Error in palm_quicksave (/home/brain/palm-alpha112/palm_quicksave.m:163->palm_miscwrite)
> Error in palm_core (/home/brain/palm-alpha112/palm_core.m:1569->palm_quicksave)
> Error in palm (/home/brain/palm-alpha112/palm.m:81->palm_core)
>
> Any suggestions?
> Thanks.
> Darren
>
> Potentially relevant information:
>
> DesignGrpContr.con =
>
> /NumWaves 3
> /NumPoints 3
> /Matrix
> 1 -1 0
> 1 0 -1
> 0 1 -1
>
> Design.mat = same as used earlier (space separated variable format)
>
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--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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