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wanderine / BROCCOLI

BROCCOLI: Software for Fast fMRI Analysis on Many-Core CPUs and GPUs
GNU General Public License v3.0
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Loading data for RandomiseGroupLevel #35

Closed cmehta126 closed 7 years ago

cmehta126 commented 7 years ago

I am performing permutation tests on results and want to use RandomiseGroupLevel. To test it out, I placed placed spatial volumes (beta-maps) for 10 subjects into a single nifti file and then created files for design/contrast matrices for 10 subjects. I ran the following to test the program.

RandomiseGroupLevel a.nii -design design.mat -contrasts design.con

The output was:

Warning: No mask being used, doing permutations for all voxels. Input data is a single volume, nothing to permute!

I am not using a mask in this test. But, there are definitely 10 volumes in the "a.nii" file. Does this commonly occur?

I created the "a.nii" file by using AFNI's 3dbucket to compile them and then 3dAFNItoNIFTI to convert to nifti format. Could this be a source of error?

Thank you.

wanderine commented 7 years ago

Can you run

3dinfo a.nii

and send me the output

Den 28 mars 2017 19:37 skrev "cmehta126" notifications@github.com:

I am performing permutation tests on results and want to use RandomiseGroupLevel. To test it out, I placed placed spatial volumes (beta-maps) for 10 subjects into a single nifti file and then created files for design/contrast matrices for 10 subjects. I ran the following to test the program.

RandomiseGroupLevel a.nii -design design.mat -contrasts design.con

The output was:

Warning: No mask being used, doing permutations for all voxels. Input data is a single volume, nothing to permute!

I am not using a mask in this test. But, there are definitely 10 volumes in the "a.nii" file. Does this commonly occur?

I created the "a.nii" file by using AFNI's 3dbucket to compile them and then 3dAFNItoNIFTI to convert to nifti format. Could this be a source of error?

Thank you.

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cmehta126 commented 7 years ago

Thank you for the quick reply. I think I just figured out a solution. Instead of using 3dbucket for combining beta-maps for subjects, I combined them with "3dTcat" and the Broccoli program is able to read the data. The "3dTcat" represents the combined volumes as a 3d-time series, whereas "3dbucket" does not represent them as such in the header. It is likely the Nifti reader in Broccoli does not like that.