4D NIFTI file for TBSS permutations testing

[rsavjanimdphd]

I am trying to use BROCCOLI to speed up permutations testing for TBSS on skeletonized WM data. I was able to run permutations testing successfully on my platform and device (AMD GPU) with your sample data:

BROCCOLI/code/testing_scripts/randomise/betas49.nii.gz

However, when I now try with my own 4D NIFTI file consisting of FA data registered to a group-derived template, I get an error stating that there are 0 possible permutations, even when just attempting -groupmean (which is meaningless for FA data). It does read in the correct dimensions of my file, and does find the correct # of subjects (n = 84) in the 4th dimension.

Command: RandomiseGroupLevel all_FA_skeletonised.nii.gz -groupmean -platform 0 -device 0 -permutations 10000 -output tbss_parallel -verbose

Output: Warning: No mask being used, doing permutations for all voxels. It took 64.409843 seconds to read the nifti file(s) Warning: Number of possible sign flips for group mean is 0, but 10000 permutations were requested. Lowering number of permutations to number of possible sign flips. Authored by K.A. Eklund Data size: 176 x 512 x 512 x 84 Number of permutations: 0 Number of regressors: 1 Number of contrasts: 1

Here also are info output on my dataset:

fslinfo all_FA_skeletonised.nii.gz: data_type FLOAT32 dim1 176 dim2 512 dim3 512 dim4 84 datatype 16 pixdim1 1.000000 pixdim2 0.500000 pixdim3 0.500000 pixdim4 1.000000 cal_max 1.5417 cal_min 0.0000 file_type NIFTI-1+

3dinfo all_FA_skeletonised.nii.gz: Dataset File: all_FA_skeletonised.nii.gz Identifier Code: NII__AL_eWytYUadLGoiKqBqBQ Creation Date: Wed Apr 22 09:02:21 2015 Template Space: ORIG Dataset Type: Echo Planar (-epan) Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST] Storage Mode: NIFTI Storage Space: 15,502,147,584 (16 billion [giga]) bytes Geometry String: "MATRIX(1,0,0,-91.02654,0,-0.5,0,94.37949,0,0,0.5,-146.8557):176,512,512" Data Axes Tilt: Plumb Data Axes Orientation: first (x) = Right-to-Left second (y) = Posterior-to-Anterior third (z) = Inferior-to-Superior [-orient RPI] R-to-L extent: -91.027 [R] -to- 83.973 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -161.121 [A] -to- 94.379 [P] -step- 0.500 mm [512 voxels] I-to-S extent: -146.856 [I] -to- 108.644 [S] -step- 0.500 mm [512 voxels] Number of time steps = 84 Time step = 1.00000s Origin = 0.00000s -- At sub-brick #0 '?' datum type is float -- At sub-brick #1 '?' datum type is float -- At sub-brick #2 '?' datum type is float \ For info on all 84 sub-bricks, use '3dinfo -verb' **

Any ideas why this might be happening? Many thanks!

[rsavjanimdphd]

Ah, I found the issue. The MAX_PERM or SIGN_FLIPS is only allocated a unsigned long int (32 bits). With n > 32, n! and 2^n will exceed 32 bits of space. To circumvent this, I added skipped calculating the max # of permutations or sign flips if n > 32. Thanks!

[wanderine]

Yes, sorry for the bug. I'm about to fly from the US to europe, will try to fix it during the weekend. Den 22 apr 2015 18:10 skrev "rickyman12" notifications@github.com:

Ah, I found the issue. The MAX_PERM or SIGN_FLIPS is only allocated a unsigned long int (32 bits). With n > 32, n! and 2^n will exceed 32 bits of space. To circumvent this, I added skipped calculating the max # of permutations or sign flips if n > 32. Thanks!

— Reply to this email directly or view it on GitHub https://github.com/wanderine/BROCCOLI/issues/17#issuecomment-95250666.

[wanderine]

This has finally been fixed.