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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Alireza
October 03, 2021 05:55PM
Thank you, Daniel.
Item four worked for me. However, I used 3dresample after 3dAllineate, too. These are the commands I used:

align_epi_anat.py -anat brain.nii.gz -epi fmri.nii -epi_base 5 -volreg off -tshift off -anat_has_skull no -epi_strip None

3dSurf2Vol -spec std.141.brain.spec -surf_A smoothwm -surf_B pial -grid_parent brain.nii.gz -sv brain.nii.gz -map_func ave -f_steps 20 -f_index points -sdata_1D mask.1d.dset -prefix mask.nii.gz

3dAllineate -prefix align_mask.nii.gz -source mask.nii.gz -NN -1Dmatrix_apply brain_al_mat.aff12.1D

3dresample -master fmri.nii -prefix final_mask.nii.gz -input align_mask.nii.gz



Edited 1 time(s). Last edit at 10/03/2021 06:01PM by Alireza.
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Align mask with EPI image Attachments

Alireza September 27, 2021 06:33PM

Re: Align mask with EPI image

Daniel Glen September 28, 2021 12:34PM

Re: Align mask with EPI image

Alireza October 03, 2021 05:55PM

Re: Align mask with EPI image

Daniel Glen October 04, 2021 12:47AM

Re: Align mask with EPI image Attachments

Alireza October 05, 2021 05:39PM

Re: Align mask with EPI image

Daniel Glen October 07, 2021 01:04PM

Re: Align mask with EPI image

Alireza November 02, 2021 06:11PM