Dear FSL experts, 

 

I am trying to use PALM to test whether two conditions evoke distinct activation patterns within a particular brain region. I have a 4D COPE for each condition containing 3D images for all subjects. My design matrix is a one-sample t-test. Here is the command I entered to run PALM: 

 

/palm-alpha56/palm -i cope1.nii -i cope2.nii -o group_avg -m striatum_1p8_iso.nii -d design.mat -t design.con -mv HotellingTsq -T -n 2000 

 

I thought that this would show me whether the activation patterns were distinct. But my PALM output is not generating the requested number of permutations so I am not sure what went wrong. Any help would be much appreciated regarding how to correctly run PALM and whether this is the right approach to answer my question. 

 

Thanks,

Sally 

.......................................................................

Running PALM alpha56 using MATLAB with the following options:

-i ../cope1.nii

-i ../cope2.nii

-o group_avg

-m ../striatum_1p8_iso.nii

-d ../../L3_para_cope1_2_NEW.gfeat/design_new.mat

-t ../../L3_para_cope1_2_NEW.gfeat/design_new.con

-mv HotellingTsq

-T

-n 2000

Found FSL in /usr/share/fsl/5.0

Reading input 1/2: ../cope1.nii

Reading input 2/2: ../cope2.nii

Testing rank of the data for the MV tests. To skip, use -noranktest.

Reading design matrix and contrasts.

Elapsed time parsing inputs: ~ 1.20512 seconds.

Number of possible permutations is 1.

Generating 1 shufflings (permutations only).

Building null distribution.

50%  [Design 1/1, Contrast 1/1, Shuffling 1/1, Modality 1/2]

     Saving file: group_avg_vox_tstat_m1

100% [Design 1/1, Contrast 1/1, Shuffling 1/1, Modality 2/2]

     Saving file: group_avg_vox_tstat_m2

     [Design 1/1, Contrast 1/1, Shuffling 1/1, Multivariate]

     Saving file: group_avg_vox_mv_hotellingtsq

Elapsed time with permutations: ~ 1.24039 seconds.

Computing p-values.

Saving p-values (uncorrected, and corrected within modality and within contrast).

     Saving file: group_avg_vox_tstat_uncp_m1

     Saving file: group_avg_vox_tstat_fwep_m1

     Saving file: group_avg_tfce_tstat_m1

     Saving file: group_avg_tfce_tstat_uncp_m1

     Saving file: group_avg_tfce_tstat_fwep_m1

     Saving file: group_avg_vox_tstat_uncp_m2

     Saving file: group_avg_vox_tstat_fwep_m2

     Saving file: group_avg_tfce_tstat_m2

     Saving file: group_avg_tfce_tstat_uncp_m2

     Saving file: group_avg_tfce_tstat_fwep_m2

Saving p-values for classical multivariate (uncorrected and corrected within contrast).

     Saving file: group_avg_vox_mv_hotellingtsq_uncp

     Saving file: group_avg_vox_mv_hotellingtsq_fwep

     Saving file: group_avg_tfce_mv_hotellingtsq

     Saving file: group_avg_tfce_mv_hotellingtsq_uncp

     Saving file: group_avg_tfce_mv_hotellingtsq_fwep

Elapsed time generating and saving results: ~ 0.551953 seconds.

Overall elapsed time: ~ 2.99747 seconds.

PALM finished at 31-Aug-2015 14:43:57.