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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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
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
| December 20, 2019 01:00PM | |
Hi AFNI experts,
I have a problem with 3dQwarp command in trying to allineate on of the slice of my functional with my anatomical images. I am working with primate and I am using a pipeline called sammba MRI that use afni.
The weird thing is that 3dQwarp command has works very well for all the slices of my primate and all the other primates. I don't really understand the error message.
Thank you very much for your help and Merry Christmas !
Clément
I have a problem with 3dQwarp command in trying to allineate on of the slice of my functional with my anatomical images. I am working with primate and I am using a pipeline called sammba MRI that use afni.
The weird thing is that 3dQwarp command has works very well for all the slices of my primate and all the other primates. I don't really understand the error message.
Thank you very much for your help and Merry Christmas !
RuntimeError: Command: 3dQwarp -allineate -allineate_opts '-parfix 1 0 -parfix 2 0 -parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6 0 -parfix 7 0 -parfix 9 0 -parfix 10 0 -parfix 12 0' -base /Documents/3_Nifti/lastV/nipype_mem/nipype-interfaces-afni-preprocess-Qwarp/ccaacfa1c8e86187e4d4dccbf5d244e8/anatT1_unifized_shr_warped_oblique_slice_0020_resampled.nii.gz -blur 0.0 2.0 -source /Documents/3_Nifti/lastV/nipype_mem/nipype-interfaces-afni-preprocess-Qwarp/ccaacfa1c8e86187e4d4dccbf5d244e8/BOLD_restingstate_tshift_volreg_oblique_tstat_n4_slice_0020_resampled.nii.gz -nmi -noXdis -noneg -prefix /Documents/3_Nifti/lastV/per_slice/BOLD_restingstate_tshift_volreg_oblique_tstat_n4_slice_0020_resampled_qwarped.nii.gz -verb Standard output: Standard error: ++ OpenMP thread count = 15 ++ 3dQwarp: AFNI version=AFNI_19.3.16 (Dec 12 2019) [64-bit] ++ Authored by: Zhark the (Hermite) Cubically Warped ++ ############################################################### + Starting 3dAllineate (affine register) command: 3dAllineate -base /Documents/3_Nifti/lastV/nipype_mem/nipype-interfaces-afni-preprocess-Qwarp/ccaacfa1c8e86187e4d4dccbf5d244e8/anatT1_unifized_shr_warped_oblique_slice_0020_resampled.nii.gz -source /Documents/3_Nifti/lastV/nipype_mem/nipype-interfaces-afni-preprocess-Qwarp/ccaacfa1c8e86187e4d4dccbf5d244e8/BOLD_restingstate_tshift_volreg_oblique_tstat_n4_slice_0020_resampled.nii.gz -prefix AFN_mK9KLDRv4rCVpGViQbjxHA.nii -1Dmatrix_save AFN_mK9KLDRv4rCVpGViQbjxHA -cmass -final wsinc5 -float -master BASE -twobest 7 -verb -parfix 1 0 -parfix 2 0 -parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6 0 -parfix 7 0 -parfix 9 0 -parfix 10 0 -parfix 12 0 -zclip -fineblur 4.44 + ############################################################### ++ 3dAllineate: AFNI version=AFNI_19.3.16 (Dec 12 2019) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: /Documents/3_Nifti/lastV/nipype_mem/nipype-interfaces-afni-preprocess-Qwarp/ccaacfa1c8e86187e4d4dccbf5d244e8/BOLD_restingstate_tshift_volreg_oblique_tstat_n4_slice_0020_resampled.nii.gz ++ Base dataset: /Documents/3_Nifti/lastV/nipype_mem/nipype-interfaces-afni-preprocess-Qwarp/ccaacfa1c8e86187e4d4dccbf5d244e8/anatT1_unifized_shr_warped_oblique_slice_0020_resampled.nii.gz ++ Loading datasets ++ 708 voxels in source_automask+0 ++ Zero-pad: not needed (plenty of internal padding) + 2D image registration: orientation is axial ++ Computing -autobox + Weightize: xfade=6 yfade=6 zfade=0 + Weightize: (unblurred) top clip=0 + Weightize: (blurred) bot clip=0 ** FATAL ERROR: Can't compute autoweight: max value seen as 0 ** Program compile date = Dec 12 2019 ** FATAL ERROR: 3dQwarp: 3dAllineate command failed** Program compile date = Dec 12 2019
Clément
| Subject | Author | Posted |
|---|---|---|
|
Doughboys | December 20, 2019 01:00PM |
|
rick reynolds | December 23, 2019 10:51AM |
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Doughboys | December 30, 2019 11:54AM |
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Doughboys | December 30, 2019 12:08PM |
|
rick reynolds | December 30, 2019 04:17PM |
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Doughboys | December 31, 2019 04:38PM |
|
rick reynolds | January 03, 2020 08:46PM |
