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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mniqureshi
October 09, 2018 11:51AM
Hello AFNI experts,

I want to preprocess my data in native space using AFNI to generate the connectivity maps.

My dataset has the following parameters:
TR = 0.681ms, and Time Points = 870, slice thickness is 2.5mm
I used the following command:

afni_proc.py -subj_id MCSA1_notlrc.rest -dsets BS0001MC_RSN.nii -copy_anat BS0001MC_t1.nii -blocks despike tshift align volreg blur mask regress -tcat_remove_first_trs 3 -tshift_interp -Fourier -blur_size 3 -regress_motion_per_run -volreg_align_e2a -regress_anaticor -regress_censor_motion 0.5 -regress_censor_outliers 0.1 -regress_bandpass 0.005 0.05 -regress_apply_mot_types demean deriv -regress_run_clustsim yes -regress_est_blur_epits -regress_est_blur_errts

Unfortunately, I can not understand the output

Please help me to choose the correct input file for the 3dNetCorr from the afni_proc.py output

Whenever I try to overlay the output file on skull-stripped anat data I see the message to perform the following command
3dwarp -deoblique

Please help me to understand and rectify these errors.

Thank you.
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Subject Author Posted

Preprocesing of multiband data

mniqureshi October 09, 2018 11:51AM

Re: Preprocesing of multiband data

rick reynolds October 24, 2018 09:00AM