AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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andek
November 20, 2013 10:27AM
Dear AFNI community,

We have been developing an open-source parallel processing software package for fMRI analysis (that we have named BROCCOLI) and we are finalizing a manuscript comparing our algorithms with other open-source packages (SPM, FSL, AFNI). The goal is not to have “winners,” but to highlight the advantages and limitations of parallel CPU and GPU-based processing. Since BROCCOLI is written in OpenCL (Open Computing Language), we are benchmarking with an Intel CPU, an Nvidia GPU and an AMD GPU.

We have compared BROCCOLI to your software in a number of different ways, and we are posting our commands in the hopes of getting a sanity-check confirmation that our usage (below) is representative of methods and command-line arguments commonly used by the AFNI community. We used the OpenMP version of AFNI to measure processing times using multi-core processing.

Thank you in advance for any comments and suggestions you may have.

Here is what we have run:

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Motion correction, linear interpolation

3dvolreg -float -linear -1Dfile motion_parameters.1D -prefix AFNI_motion_corrected.nii infile.nii

Motion correction, Fourier interpolation

3dvolreg -float -1Dfile motion_parameters.1D -prefix AFNI_motion_corrected.nii infile.nii

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Normalization

3dUnifize -GM -prefix MNI_unifized.nii -input MNI_TEMPLATE

3dUnifize -GM -prefix anat_unifized.nii -input anat.nii

3dAllineate -prefix anat_affine.nii -base MNI_unifized.nii -source anat_unifized.nii -source_automask -twopass -cost lpa -1Dmatrix_save anat_affine.1D -autoweight -fineblur 3 -cmass

3dQwarp -duplo -useweight -nodset -blur 0 3 -prefix AFNI_warped.nii -source anat_affine.nii -base MNI_unifized.nii

Linear interpolation

3dNwarpApply -interp linear -nwarp AFNI_warped_WARP.nii -affter anat_affine.1D -source anat.nii -master MNI_TEMPLATE -prefix AFNI_warped.nii

Sinc interpolation

3dNwarpApply -nwarp AFNI_warped_WARP.nii -affter anat_affine.1D -source anat.nii -master MNI_TEMPLATE -prefix AFNI_warped.nii

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First level analysis, through afni_proc.py

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For further details, see our github repository. Also please feel free to try out our software (see the beta testing folder) and comment on that as well.

[github.com]

Regards,
Anders Eklund
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A new fMRI software - BROCCOLI

andek November 20, 2013 10:27AM