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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:

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Sincerely, AFNI HQ

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jkblujus
September 29, 2021 03:10PM
Hi AFNI team,

I am preprocessing resting state data from an older sample. I am using AFNI_21.2.04 version and my proc.py command can be found below. When examining the HTML output I saw that for the TSNR images in some participants the highest values are localized to the white matter. Is this odd? How would you expect the distribution of values to be according to the tissue types (e.g., highest in GM, lower in WM/CSF)? I've attached an example image of the output here.

Thanks,
Jenna 

afni_proc.py                                                                                                           	 \
                 -subj_id sub01 -script proc.sub01 -scr_overwrite -out_dir sub01.results     \
                 -blocks despike tshift align tlrc volreg blur mask scale                               \
                     regress                                                                                            	\
                 -radial_correlate_blocks tcat volreg                                                             \
                 -copy_anat ${ss_dir}/anatSS.sub01.nii                                                         \
                 -anat_has_skull no                                                                                      \
                 -anat_follower anat_w_skull anat  ${ss_dir}/anatU.sub01.nii                       \
                 -anat_follower_ROI aaseg anat ${fs_dir}/aparc.a2009s+aseg.nii.gz           \
                 -anat_follower_ROI aeseg epi ${fs_dir}/aparc.a2009s+aseg.nii.gz            \
                 -anat_follower_ROI FSvent epi ${fs_dir}/fs_ap_latvent.nii.gz                     \
                 -anat_follower_ROI FSWe epi ${fs_dir}/fs_ap_wm.nii.gz                            \
                 -anat_follower_erode FSvent FSWe                                                            \
                 -dsets ${raw_epi}                                                                                      \
                 -tcat_remove_first_trs 4                                                                               \
                 -tshift_opts_ts -tpattern altplus						      \
                 -align_opts_aea -cost lpc+ZZ -giant_move -check_flip                                   \
                 -tlrc_base MNI152_2009_template_SSW.nii.gz                                              \
                 -tlrc_NL_warp                                                                                          \
                 -tlrc_NL_warped_dsets ${ss_dir}/anatQQ.sub01.nii ${ss_dir}/anatQQ.sub01.aff12.1D                     \
                     ${ss_dir}/anatQQ.sub01_WARP.nii                                                               \
                 -volreg_align_to MIN_OUTLIER                                                                       \
                 -volreg_align_e2a                                                                                      \
                 -volreg_tlrc_warp                                                                                      \
                 -blur_size 4                                                                                           \
                 -mask_epi_anat yes                                                                                     \
                 -regress_motion_per_run                                                                                \
                 -regress_ROI_PC FSvent 3                                                                               \
                 -regress_ROI_PC_per_run FSvent                                                                     \
                 -regress_make_corr_vols aeseg FSvent                                                             \
                 -regress_anaticor_fast                                                                                 \
                 -regress_anaticor_label FSWe                                                                           \
                 -regress_censor_motion 0.3										\
 	      	 -regress_censor_outliers 0.1										\
		 -regress_bandpass 0.01 0.1                                                                             \
                 -regress_apply_mot_types demean deriv                                                            \
                 -regress_est_blur_epits                                                                                \
                 -regress_est_blur_errts                                                                                \
                 -html_review_style pythonic
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Subject Author Posted

TSNR overlay Attachments

jkblujus September 29, 2021 03:10PM

Re: TSNR overlay

rick reynolds October 05, 2021 04:17PM