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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JW
November 24, 2019 05:22PM
Dear AFNI experts,

Below is the script we used to preprocess my EPI (task-based) data. We are looking for pre-processed but non-statistically analyzed data so we removed regress options.

afni_proc.py \
-anat_has_skull yes \
-blocks despike tshift align tlrc volreg mask scale regress \
-copy_anat mprage/mprage.${subj}.${cond}+orig \
-dsets /Users/lab/Desktop/AES2016_FNT/${subj}/${subj}.${cond}/FNT/fnt.${subj}.${cond}+orig \
-out_dir Purcell_result_without_regress_glt \
-script py_result_${subj}.${cond}.script \
-scr_overwrite \
-subj_id ${subj} \
-verb 2 \
-align_opts_aea -deoblique off -giant_move -Allineate_opts -usetemp \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_opts_at -ok_notice -dxyz 1 -pad_base 100 -init_xform AUTO_CENTER \
-tlrc_suffix _MNI152 \
-volreg_align_to third \
-volreg_interp -Fourier \
-volreg_opts_vr -twopass -noclip -dfile volreg.${subj}.${cond}.1d \
-volreg_tlrc_warp \
-volreg_warp_dxyz 3

When I checked the data quality, I see some discrepancies between the volreg data and MNI space (see attached picture). Could you please let me know how to address this gap?

Sorry, I accidentally posted two same messages. Could you please delete the above?

Best,
JW



Edited 2 time(s). Last edit at 11/24/2019 05:32PM by JW.
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EPI registration Attachments

JW November 24, 2019 05:22PM

Re: EPI registration

ptaylor November 28, 2019 03:43AM