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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