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

History of AFNI updates  

|
April 03, 2020 11:24AM
Hi Paul,

I edited the afni_proc.py scripts according to your suggestions but my alignment from QC html looks different from your attachment.

The script:
afni_proc.py \
-subj_id {$subj} \
-script proc.{$subj}.vwfa \
-out_dir {$subj}.VWFA.results \
-dsets {$subj}_vwfa_1+orig {$subj}_vwfa_2+orig \
-copy_anat {$subj}_2_t1+orig \
-anat_has_skull yes \
-blocks despike tshift align volreg blur mask scale regress \
-tcat_remove_first_trs 5 \
-tshift_interp -Fourier \
-volreg_align_to MIN_OUTLIER \
-align_opts_aea \
-cmass cmass \
-volreg_align_e2a \
-regress_stim_times word.txt checkerboard.txt \
-regress_local_times \
-regress_stim_labels word checkerboard \
-regress_basis 'BLOCK(24,1)' \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_opts_3dD \
-jobs 4 \
-gltsym 'SYM: +word -checkerboard' \
-glt_label 1 word_vs_checkerboard \
-regress_run_clustsim no \
-regress_est_blur_errts \
-regress_est_blur_epits \
-html_review_style pythonic
Attachments:
open | download - C05_epi_to_anat.jpg (130.9 KB)
Subject Author Posted

Alignment problem with afni_proc.py Attachments

joy0617 March 28, 2020 04:06PM

Re: Alignment problem with afni_proc.py

ptaylor March 28, 2020 05:40PM

Re: Alignment problem with afni_proc.py

joy0617 March 29, 2020 11:59AM

Re: Alignment problem with afni_proc.py

ptaylor March 29, 2020 01:15PM

Re: Alignment problem with afni_proc.py

joy0617 March 30, 2020 10:16AM

Re: Alignment problem with afni_proc.py

ptaylor March 30, 2020 10:43AM

Re: Alignment problem with afni_proc.py Attachments

joy0617 April 02, 2020 04:12PM

Re: Alignment problem with afni_proc.py

ptaylor April 02, 2020 07:02PM

Re: Alignment problem with afni_proc.py Attachments

ptaylor April 03, 2020 10:27AM

Re: Alignment problem with afni_proc.py Attachments

joy0617 April 03, 2020 11:24AM

Re: Alignment problem with afni_proc.py

ptaylor April 03, 2020 12:01PM

Re: Alignment problem with afni_proc.py Attachments

ptaylor April 04, 2020 12:09PM

Re: Alignment problem with afni_proc.py

joy0617 April 05, 2020 01:25PM

Re: Alignment problem with afni_proc.py Attachments

joy0617 March 29, 2020 12:03PM