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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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Ilaria
March 05, 2019 02:15PM
Hello,

I am checking the alignment between the final anatomical and the full mask for each participant to ensure that coverage is appropriate. I have a couple of instances where the coverage is really off and others where some voxels appear around the actual brain.
What may I do to improve the coregistration? Finally, how much off is acceptable? For example, would sub-020 in the picture be considered OK or would you preprocess differently?

My current proc.py is 
afni_proc.py -subj_id $subj_id                          \
              -blocks tshift align tlrc volreg blur mask scale 	  \
              regress 											  \
              -copy_anat $data_root/$subj_id/$session/anat/sub-0??_ses-T?_T1w.nii.gz \
              -dsets                                              \
                  $data_root/$subj_id/$session/func/sub-0??_ses-T?_task-Num_run-0?_bold.nii.gz \
              -align_opts_aea -cost lpc+ZZ                        \
              -tshift_interp -quintic   						  \
              -tlrc_base HaskinsPeds_NL_template1.0+tlrc          \
              -tlrc_NL_warp                                       \
              -volreg_align_to MIN_OUTLIER                        \
              -volreg_align_e2a                                   \
              -volreg_tlrc_warp                                   \
              -regress_motion_per_run                             \
              -regress_censor_motion 0.6                          \
              -regress_censor_outliers 0.1						  \
              -regress_censor_prev no                             \
              -regress_reml_exec 				                  \
              -regress_stim_times                                 \
		         $data_root/$subj_id/$session/stim/Easy.*         \
                 $data_root/$subj_id/$session/stim/Medium.*       \
                 $data_root/$subj_id/$session/stim/Hard.*         \
                 $data_root/$subj_id/$session/stim/control_n.*    \
              -regress_stim_labels                                \
                  LargeD MediumD SmallD Ctrl_n                    \
              -regress_basis GAM            		              \
              -regress_opts_3dD                                   \
                  -bout                                           \
                  -jobs 4                                         \
                  -gltsym 'SYM: SmallD -LargeD' -glt_label 1 Small-Large  \
                  -gltsym 'SYM: SmallD -MediumD' -glt_label 2 Small-Medium  \
                  -gltsym 'SYM: MediumD -LargeD' -glt_label 3 Medium-Large  \
                  -gltsym 'SYM: SmallD MediumD LargeD -3*Ctrl_n' -glt_label 4 All-control \
                  -gltsym 'SYM: LargeD -Ctrl_n' -glt_label 5 Large-Control \
                  -gltsym 'SYM: SmallD -Ctrl_n' -glt_label 6 Small-Control \
                  -gltsym 'SYM: MediumD -Ctrl_n' -glt_label 7 Medium-Control \
              -regress_est_blur_epits							  \
              -regress_est_blur_errts                             \
              -write_3dD_prefix stats.MoreContrasts               \
              -execute

Thank you!
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Attachments:
open | download - NonAligned2.png (149.3 KB)
open | download - AlignmentProblem.png (152.7 KB)
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Subject Author Posted

full mask issues Attachments

Ilaria March 05, 2019 02:15PM

Re: full mask issues

Daniel Glen March 05, 2019 05:20PM

Re: full mask issues

Ilaria March 05, 2019 10:16PM

Re: full mask issues

ptaylor March 05, 2019 10:30PM

Re: full mask issues Attachments

Ilaria March 06, 2019 09:26AM

Re: full mask issues

ptaylor March 06, 2019 10:10AM

Re: full mask issues

Ilaria March 06, 2019 10:25AM

Re: full mask issues

ptaylor March 06, 2019 10:50AM

Re: full mask issues

Ilaria March 08, 2019 03:57PM

Re: full mask issues

ptaylor March 08, 2019 06:48PM