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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wo222
October 23, 2017 02:41PM
Dear AFNI experts,

I am new to AFNI and struggle to figure out where the statistic map is saved after running afni_proc.py without multiple testing. Is it one of the images within stats.${subject}_REML? I run afni_proc.py with the following options (canonical HRF with derivative):

afni_proc.py \
-subj_id $subject \
-script proc.$subject -scr_overwrite \
-tcat_remove_first_trs 0 \
-dsets ${path_data}/${subject}_${task}_bold.nii \
-blur_size $smoothing.0 \
-regress_stim_types AM1 \
-regress_stim_times \
${path_manage}/experimental_designs/${study}_${exper_design}.txt \
-regress_stim_labels boxcar_1 \
-regress_basis 'SPMG2' \
-regress_opts_3dD \
-jobs 1 \
-regress_make_ideal_sum sum_ideal.1D \
-volreg_align_to third \
-regress_run_clustsim no \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_reml_exec \
-regress_opts_reml -Rwherr whitened_errts.${subject}_REML

I guess this command of mine (adapted from some template) could be conciser...

Sorry for bothering you!

Best,

Wiktor
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Subject Author Posted

where is the z or t statistic map?

wo222 October 23, 2017 02:41PM

Re: where is the z or t statistic map? Attachments

wo222 October 24, 2017 01:43PM

Re: where is the z or t statistic map?

wo222 October 25, 2017 12:21PM