[caret-users] t-test iteration quits

[John Harwell]

Akiko,

We do limit the number of iterations to "2 to the Nth power" where N  
is the number of columns in the input metric file.  If you are being  
limited to 16 iterations, it implies that your metric file contains 4  
columns.  To create the randomized file for the one-sample T-Test,  
each column of data is multiplied by a positive or negative one.    
Since each column has two possible values, "2 to the N" is the maximum  
number of unique permutations.  See pages 18-20 of Nonparametric  
Permutation Tests for Functional Neuroimaging: A Primer with Examples  
by Thomas E. Nichols and Andrew P. Holmes in Human Brain Mapping  
15:1-25 (2001).

However, if you have more than four columns in your metric file, try  
the latest version of Caret, 5.611, available from http://brainvis.wustl.edu/wiki/index.php/Caret:Download 
.  Note that the command "-metric-or-shape-stat-one-sample-t-test" has  
been renamed to "-metric-statistics-one-sample-t-test".  If the  
problem still occurs, please let us know.

-----------------------------------
John Harwell
john at brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jul 16, 2009, at 6:04 PM, Akiko Ikkai wrote:

> Hi,
>
> I'm trying to run one-sample t-test from the command line, and  
> having this strange problem of iteration quitting at 16th  
> permutation, or fewer. If I give iteration fewer than 16, it runs  
> fine, but anything above it, it quits at 16. I can't seem to find  
> where this magic number 16 is coming from. Below is the command I'm  
> running:
>
> for EACHMETRIC in `ls *LH*.metric`;
> do
> /usr/local/caret-5.51/bin/caret_command -metric-or-shape-stat-one- 
> sample-t-test ${EACHMETRIC} /hyper/library/caret_files/ 
> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_711-2C.clean.align. 
> 73730.coord /hyper/library/caret_files/Human.sphere_6.LEFT_HEM. 
> 73730.topo /hyper/library/caret_files/ 
> deformed.Human.LH.Group.surface_shape 3 T-Map_${EACHMETRIC}  
> Permuted_T-Map_${EACHMETRIC} `basename ${EACHMETRIC} .metric`.paint  
> T-Stats_`basename ${EACHMETRIC} .metric`.metric T-Stats_`basename $ 
> {EACHMETRIC} .metric`.txt -2.5 2.5 0.1 10 1 100 0 4 ;
> done
>
> we are running caret version 5.51 on Mac.
> ... any insights?
>
> Thanks in advance! Akiko
>
> Akiko Ikkai
> PhD Candidate
> Department of Psychology
> New York University
> 6 Washington Place
> New York NY, 10003
>
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