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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tamtam
August 29, 2018 02:06PM
Thank you Rick. I ran @SSwarper and the jpeg files look reasonable. When I tried to feed the inputs back into my afni_proc.py script however, it resulted in an error message indicating that the +tlrc warp dataset was missing. It seems afni_proc.py was trying to find the file "anatQQ.MNI152_2009_template_SSW.nii.gz+tlrc" which I don't have.

Would it be safe to replace the endings ( "+tlrc" with ".nii") as the anatQQ.MNI152_2009_template_SSW.nii.gz.nii is the skull stripped and warped file?

afni_proc.py script I altered:

-tcat_remove_first_trs 0 -tlrc_base MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets anatQQ.MNI152_2009_template_SSW.nii.gz.nii anatQQ.MNI152_2009_template_SSW.nii.gz.aff12.1D anatQQ.MNI152_2009_template_SSW.nii.gz_WARP.nii \
-volreg_align_to last -volreg_align_e2a -volreg_tlrc_warp -blur_size \
4.0 -regress_stim_times \

Thank you!
Tamara
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Subject Author Posted

Error in affine step

tamtam August 07, 2018 05:01PM

Re: Error in affine step

Peter Molfese August 07, 2018 05:17PM

Re: Error in affine step Attachments

tamtam August 08, 2018 08:31AM

Re: Error in affine step

rick reynolds August 09, 2018 09:20AM

Re: Error in affine step

tamtam August 29, 2018 02:06PM

Re: Error in affine step

ptaylor August 29, 2018 02:21PM

Re: Error in affine step

tamtam August 29, 2018 02:44PM

Re: Error in affine step

ptaylor August 29, 2018 03:02PM

Re: Error in affine step

tamtam August 29, 2018 03:56PM

Re: Error in affine step

ptaylor August 29, 2018 04:42PM

Re: Error in affine step

tamtam August 30, 2018 10:01AM

Re: Error in affine step

ptaylor August 30, 2018 10:50AM

Re: Error in affine step

tamtam August 31, 2018 08:26AM