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  

|
June 07, 2022 03:20AM
Hello!

I've been trying to pre-process some pilot data from a Hariri faces task (alternating blocks of shapes and faces).

I've used the following to generate a script:
module load afni/21.1.07
module load anaconda/3.8
-----------------------------------------
afni_proc.py -blocks despike tshift align tlrc volreg blur mask scale regress -copy_anat t1.nii.gz -anat_has_skull yes -dsets hariri.nii.gz -tcat_remove_first_trs 2 -align_opts_aea -cost nmi -skullstrip_opts -push_to_edge -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp -volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -mask_epi_anat yes -mask_segment_anat yes -mask_segment_erode yes -blur_size 6 -blur_in_mask yes -regress_bandpass 0.01 0.1 -regress_ROI WMe CSF -regress_stim_times stim_t_shapes stim_t_faces -regress_stim_labels shapes faces -regress_motion_per_run -regress_censor_motion 0.3 -regress_censor_outliers 0.05 -regress_apply_mot_types demean deriv -regress_3dD_stop -regress_reml_exec -regress_compute_fitts -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no -html_review_style pythonic

I've also removed the -tzero 0 part and added the following to the 3dTshift bit:
-TR 2.0s -tpattern seqminus

When checking the QC report, I noticed that there are only speckles in the vstat image (attached). The subject didn't move much (only volumes 2 and 3 were censored), they didn't fall asleep and they did the task correctly. Therefore, I expected to see something substantial in the visual areas, but alas..

I've also attached an image of the regressors and the warning that I got.

I'm not exactly sure what I'm doing wrong, so any help would be highly appreciated!

Cheers,
Misho
Attachments:
open | download - vstat.png (1.96 MB)
open | download - regressors_warning.png (611.3 KB)
Subject Author Posted

Speckles in vstat - Hariri faces task Attachments

misho_dimitrov June 07, 2022 03:20AM

Re: Speckles in vstat - Hariri faces task

rick reynolds June 07, 2022 09:37AM

Re: Speckles in vstat - Hariri faces task

misho_dimitrov June 08, 2022 03:26AM

Re: Speckles in vstat - Hariri faces task

misho_dimitrov June 08, 2022 05:51AM

Re: Speckles in vstat - Hariri faces task

rick reynolds June 08, 2022 02:31PM

Re: Speckles in vstat - Hariri faces task

ptaylor June 08, 2022 03:11PM

Re: Speckles in vstat - Hariri faces task

misho_dimitrov June 13, 2022 10:11AM