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Hi Sally, Indeed, this is a simple case -- a one-sample t-test -- and it should go smoothly. The step where you say it hangs (when it generates the 200 sign-flips) isn't one what would cause difficulties. Nonetheless, could you try again adding the options "-cmcx" and "-cmcp"? Thanks. All the best, Anderson On 13 December 2016 at 19:03, Durgerian, Sally <[log in to unmask]> wrote: > Hello Anderson, > Thank you for all the work you’ve done on PALM. I had it working for some > nifti data files, but when I tried a really simple case with CIFTI files, > matlab seemed to hang up before completing any of the randomizations/sign > changes. It doesn’t seem like such a difficult design that it would take a > long time. Do you have any idea what the problem might be? > Your help is much appreciated, > Sally > > Here is what I see in the matlab window (and then I can wait for hours and > not see anything more). > Running PALM alpha102 using MATLAB 8.3.0.532 (R2014a) with the following > options: > -i data.32k_fs_LR.dscalar.nii > -accel tail > -n 200 > -nouncorrected > Found FSL in /usr/share/fsl/5.0 #(note - this is version 5.0.8) > Found HCP Workbench executable in /usr/share/workbench/bin_linux64/wb_command > #(this is version 1.2.3) > Reading input 1/1: data.32k_fs_LR.dscalar.nii > Reading design matrix and contrasts. > Elapsed time parsing inputs: ~ 1.769 seconds. > Number of possible sign-flips is exp(41181.3) = 2^59412. > Generating 200 shufflings (sign-flips only). > > Here is information about the input file: > Name: data.32k_fs_LR.dscalar.nii > Type: Connectivity - Dense Scalar > Structure: CortexLeft CortexRight > Data Size: 7.37 Megabytes > Maps to Surface: true > Maps to Volume: false > Maps with LabelTable: false > Maps with Palette: true > All Map Palettes Equal: true > Map Interval Units: NIFTI_UNITS_UNKNOWN > Number of Maps: 31 > Number of Rows: 59412 > Number of Columns: 31 > Volume Dim[0]: 0 > Volume Dim[1]: 0 > Volume Dim[2]: 0 > Palette Type: Map (Unique for each map) > CIFTI Dim[0]: 31 > CIFTI Dim[1]: 59412 > ALONG_ROW map type: SCALARS > ALONG_COLUMN map type: BRAIN_MODELS > Has Volume Data: false > CortexLeft: 29696 out of 32492 vertices > CortexRight: 29716 out of 32492 vertices > > Map Minimum Maximum Mean Sample Dev % Positive % Negative > Inf/NaN Map Name > 1 0.343 4.798 1.562 0.175 100.000 0.000 > 0 sub01 > 2 1.323 3.684 2.049 0.224 100.000 0.000 > 0 sub02 > ... > 31 0.602 4.024 2.048 0.261 100.000 0.000 > 0 sub31 >