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  

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June 11, 2018 05:30PM
Hello AFNI team,

I would like to do resting state analysis on surface. I've created afni_proc.py script file for each hemisphere and I've got an error saying...** FATAL ERROR: Mask creation fails for unknown reasons!

My afni_proc.py command is below.

afni_proc.py -subj_id ${subj}_${hemisphere} \
-script proc.${subject}_${hemisphere} -scr_overwrite \
-blocks despike tshift align volreg surf blur mask regress \
-copy_anat $top_dir/${subj}_MPRAGE_wo_skull+orig \
-anat_has_skull no -tcat_remove_first_trs 0 \
-dsets \
$top_dir/${subj}.s.01_RS+orig \
$top_dir/${subj}.s.02_RS+orig \
$top_dir/${subj}.s.03_RS+orig \
$top_dir/${subj}.s.04_RS+orig \
-surf_anat /Applications/freesurfer/subjects/${subject}/SUMA/${subject}_SurfVol.nii \
-surf_spec /Applications/freesurfer/subjects/${subject}/SUMA/std.141.${subject}_${hemisphere}.spec \
-volreg_align_to third -volreg_align_e2a \
-blur_size 4 \
-regress_censor_motion 0.2 \
-regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_errts \
-regress_run_clustsim no


When I generated the script file for task related experiment, I excludes mask option. I tested this on resting state analysis on surface but I could not generate the script file without mask option (e.g. I've got an error that ** script creation failure for block 'regress').

Any suggestions?

Thanks,
Taek
Subject Author Posted

Resting state analysis on Surface

Hyuntaek June 11, 2018 05:30PM

Re: Resting state analysis on Surface

Peter Molfese June 12, 2018 10:59AM

Re: Resting state analysis on Surface

rick reynolds June 12, 2018 12:29PM

Re: Resting state analysis on Surface

Hyuntaek June 12, 2018 04:42PM

Re: Resting state analysis on Surface

rick reynolds June 14, 2018 11:43AM