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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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dmomi
May 01, 2020 12:38PM
Dear experts,

I have preprocessed a resting state fMRI using afni_proc.py with the following command 

afni_proc.py -subj_id 003_S_6264 \
 -blocks align tlrc volreg mask blur regress \
 -copy_anat /Volumes/WD_Elements/ADNI/fmri_afni/T1w_without_skull.nii.gz \
 -anat_follower_ROI vent epi /Volumes/WD_Elements/ADNI/fmri_afni/003_S_6264/SUMA/vent.nii               \
 -anat_follower_ROI wm epi /Volumes/WD_Elements/ADNI/fmri_afni/003_S_6264/SUMA/wm.nii \
 -anat_follower_erode vent wm \
 -dsets /Volumes/WD_Elements/ADNI/fmri_afni/rsFmri.nii.gz -align_opts_aea -cost lpc+ZZ \
 -volreg_align_e2a  -volreg_tlrc_warp  \
 -tlrc_opts_at -init_xform CENTER \
 -blur_size 5 -regress_polort 3 -regress_censor_outliers .1         \
 -regress_censor_motion .2 -regress_apply_mot_types demean deriv      \
 -regress_ROI_PC vent 1 -regress_ROI_PC wm 1 -regress_anaticor_fast   \
 -regress_anaticor_label wm


Everything went smoothly and also the connectivity map from the precuneus looks legit to me (see first figure attached)

However when I plot the time series thay look really weird and some time point is flat and the corresponding volume completely black (see second figure attached)

Any idea why and eventually how can i solve this?

Thanks

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Attachments:
open | download - Screen Shot 2020-05-01 at 12.34.36.png (95.9 KB)
open | download - Screen Shot 2020-05-01 at 12.37.39.png (94 KB)
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Subject Author Posted

Weird timeseries produced for resting state fMRI Attachments

dmomi May 01, 2020 12:38PM

Re: Weird timeseries produced for resting state fMRI

rick reynolds May 01, 2020 01:03PM

Re: Weird timeseries produced for resting state fMRI

dmomi May 01, 2020 02:10PM

Re: Weird timeseries produced for resting state fMRI

rick reynolds May 06, 2020 10:40AM