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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icupsy
May 19, 2021 05:52AM
Hi AFNI experts,

We preprocessed task fMRI images and fit the GLM at the individual level. When we check the statistical maps for each condition at the individual level (p < .001), some statistical maps seem not to align the anatomical images very well. For example, in the attached files which belong to the visual condition, children just passively view the characters presented on the screen. A large proportion of "activated" voxels lay outside of the brain. We also tried -giant_move option but it did not help a lot. Do you have any ideas to fix this?

Xin

The afni_proc.py cmd we used. 

afni_proc.py -subj_id s0 -script proc.av -blocks despike tshift align tlrc  \
    volreg blur mask scale regress -copy_anat                               \
    /Volumes/ana_SG/audvis/afni/ana/${subj}/anat/${subj}.anat+orig              \
    -anat_has_skull yes -dsets                                              \
    ana/${subj}/func/${subj}.run1+orig.HEAD         \
    ana/${subj}/func/${subj}.run2+orig.HEAD         \
    ana/${subj}/func/${subj}.run3+orig.HEAD         \
   ana/${subj}/func/${subj}.run4+orig.HEAD         \
    -tcat_remove_first_trs 0 -align_opts_aea -cost lpc+ZZ -big_move         \
    -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp -volreg_align_to          \
    MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size 8            \
    -regress_stim_times ****.1D \
    -regress_stim_labels phon_A phon_V phon_AVC phon_AVI char_A char_V      \
    char_AVC char_AVI -regress_basis 'BLOCK(20.8,1)' -regress_censor_motion \
    2 -regress_censor_outliers 0.10 -regress_motion_per_run                 \
    -regress_make_ideal_sum sum_ideal.1D -regress_opts_3dD -num_glt 4       \
    -gltsym 'SYM: phon_AVC -phon_AVI' -glt_label 1 phon_con -gltsym 'SYM:   \
    char_AVC -char_AVI' -glt_label 2 char_con -gltsym 'SYM: phon_AVC        \
    -phon_A -phon_V' -glt_label 3 phon_supadd -gltsym 'SYM: char_AVC        \
    -char_A -char_V' -glt_label 4 char_supadd -jobs 2                       \
    -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no
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Attachments:
open | download - mis_align.png (121.1 KB)
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Subject Author Posted

T1 and statistical map at indiviudal level not align well Attachments

icupsy May 19, 2021 05:52AM

Re: T1 and statistical map at indiviudal level not align well

ptaylor May 19, 2021 10:25AM

Re: T1 and statistical map at indiviudal level not align well Attachments

icupsy May 21, 2021 08:32AM

Re: T1 and statistical map at indiviudal level not align well

ptaylor May 24, 2021 11:48AM

Re: T1 and statistical map at indiviudal level not align well Attachments

icupsy May 24, 2021 10:40PM