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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:
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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Thanks for the reply!
So if there are no non-zero voxels the output .txt will be empty?
A couple of my ROIs have all '0' in all rows and others are empty. What would be the difference?
by
dmoracze
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AFNI Message Board
Hello,
We are trying to create a correlation matrix for 502 ROIs and 320 TRs. I have been using 3dmaskave to write the average signal over each TR. Here is my command:
3dmaskave -mask /Volumes/share/avspeech_mri/children/freesurfer/avsmri017fs/SUMA_lausanne/lausanne2008_aparc+aseg.frac+orig -q -mrange $x $x /Volumes/share/avspeech_mri/children/avsmri017/fsl/post_al/cleanedts.3mm_censor+or
by
dmoracze
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AFNI Message Board
Thank you for your response. I tried running the command with that option and got this:
@SUMA_AlignToExperiment -exp_anat avsmri017_SurfVol.al_Alnd_Exp+orig -surf_anat lausanne2008_aparc+aseg.nii -atlas_followers -align_centers
@SUMA_AlignToExperiment -exp_anat avsmri017_SurfVols_followers -align_centers
/Volumes/share/avspeech_mri/children/freesurfer/avsmri017fs/SUMA/
Adding /Volumes/s
by
dmoracze
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AFNI Message Board
We already ran @SUMA_Make_Spec_FS and added our atlas to any instance of the command calling the other atlas. If the problem may be found in this step, is there another/better way to incorporate our new atlas into the command?
by
dmoracze
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AFNI Message Board
We are trying to align a parcellation overlay from Freesurfer (e.g., lausanne2008_aparc+aseg.nii) to our SurfVol_Alnd_Exp. Here is what we have tried for subject 017.
@SUMA_AlignToExperiment -surf_anat ../../SUMA/avsmri017fs_SurfVol+orig. -al -exp_anat anat_final.avspeech+orig -align_centers -out_dxyz 0.3 -prefix avsmri017_SurfVol.al_Alnd_Exp_wd -wd
(this step works)
3dWarp -matparent
by
dmoracze
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AFNI Message Board
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Pages: 123