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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SarahChang
February 21, 2018 02:37PM
Hi Daniel,

The command I used to generate the matrix is:
3dAllineate -prefix anat_within_aligned -base ${subj}_avg_anat+orig -1Dmatrix_save align_to_avg -source anat+orig

And then I used that matrix in afni_proc.py:
afni_proc.py -subj_id $subj.vol \
-blocks tshift align volreg scale \
-copy_anat ${subj}_avg_anat+orig \
-dsets run_*+orig.HEAD \
-tcat_remove_first_trs 0 \
-align_opts_aea -pre_matrix $top_dir/align_to_avg.aff12.1D -cost lpa -partial_coverage -anat_has_skull 'no' \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-scr_overwrite \
-execute

The matrix doesn't have any problem when I did surface analysis. But when I tried to use the same matrix to do the volume based analysis, it gave me that error.

Sarah
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Subject Author Posted

A question about transformation matrix

SarahChang February 21, 2018 10:17AM

Re: A question about transformation matrix

Daniel Glen February 21, 2018 12:05PM

Re: A question about transformation matrix

SarahChang February 21, 2018 02:37PM

Re: A question about transformation matrix

SarahChang February 21, 2018 03:12PM

Re: A question about transformation matrix

Daniel Glen February 21, 2018 03:50PM