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GMan
August 02, 2019 02:11PM
Hello,

I have been given some data and within the afni analysis folder there are this file outlining the onset and duration of a stimulus presented in the first 6 runs (there are 9 runs in total):

45:30 103:33 166:36 238:39 309:33 382:39
45:30 103:33 166:36 238:39 309:33 382:39
38:30 96:33 159:36 231:39 302:33 375:39
45:30 103:33 166:36 238:39 309:33 382:39
45:30 103:33 166:36 238:39 309:33 382:39
45:30 103:33 166:36 238:39 309:33 382:39
* *
* *
* *

The afni_proc.py (see below) for the data used for the task-regression_block has used -regress stim_types AM1 and dmUBLOCK(0) as the basis function. As far as I can tell, there is no reason for amplitude modulation in this experiment- should another basis function be used instead? 


afni_proc.py -subj_id ${subj}         		                \
      -dsets ${subj}/afni_folder/f*${subj}_task*.nii.gz \
      -blocks despike tshift align tlrc volreg blur mask scale regress   \
      -copy_anat ${subj}/afni_folder/a*${subj}_T1w.nii.gz 	      \
      -align_opts_aea -cost lpc+ZZ                                \
      -tlrc_base MNI152_T1_2009c+tlrc                             \
      -tlrc_NL_warp                                               \
      -volreg_align_to MIN_OUTLIER                                \
      -volreg_align_e2a                                           \
      -volreg_tlrc_warp                                           \
      -volreg_warp_dxyz 2                                       \
      -mask_epi_anat yes                                          \
      -blur_in_automask                                           \
      -blur_to_fwhm                                               \
      -blur_size 4                                                \
      -regress_stim_times ${subj}/afni_folder/B*afni_task*.txt    \
      -regress_stim_types AM1		                                  \
                          AM1 AM1	                                \
                          AM1 AM1	                                \
                          AM1 AM1                                 \
                          AM1 AM1	                                \
                          AM1 AM1	                                \
      -regress_stim_labels                                        \
                      stim_on                                     \
                      rest15_on rest30_on                         \
                      stand15_on stand30_on                       \
                      step15_on  step30_on                        \
                      rest_sham  stand_sham                       \
                      step_sham  sham_on                          \
      -regress_local_times                                        \
      -regress_basis 'dmUBLOCK(0)'   			                        \
      -regress_apply_mot_types demean deriv                       \
      -regress_motion_per_run                                     \
      -regress_censor_motion 0.5                                 \
      -regress_compute_fitts                                      \
      -regress_reml_exec                                          \
      -regress_opts_3dD               		                        \
      -jobs 6					                                            \
      -GOFORIT 4                                                  \
      -num_glt 19                                                 \
              -gltsym 'SYM: +rest30_on -rest15_on'                         \
              -glt_label 1  rest30_vs_rest15                               \
              -gltsym 'SYM: +stand30_on -stand15_on'                       \
              -glt_label 2  stand30_vs_stand15                             \
              -gltsym 'SYM: +step30_on -step15_on'                         \
              -glt_label 3  step30_vs_step15                               \
              -gltsym 'SYM: +stand15_on -rest15_on'   		                 \
              -glt_label 4  stand_vs_rest15                   	           \
              -gltsym 'SYM: +step15_on -rest15_on'   		                   \
              -glt_label 5  step_vs_rest15                    	           \
              -gltsym 'SYM: +step15_on -stand15_on'   		                 \
              -glt_label 6  step_vs_stand15                    	           \
              -gltsym 'SYM: +stand30_on -rest30_on'   		                 \
              -glt_label 7  stand_vs_rest30                   	           \
              -gltsym 'SYM: +step30_on -rest30_on'   		                   \
              -glt_label 8  step_vs_rest30                    	           \
              -gltsym 'SYM: +step30_on -stand30_on'   		                 \
              -glt_label 9  step_vs_stand30                    	           \
              -gltsym 'SYM: +step30_on -stand30_on'   		                 \
              -glt_label 10  step_vs_stand30                    	         \
              -gltsym 'SYM: +stand30_on +stand15_on -rest15_on -rest30_on' \
              -glt_label 11  stand_vs_rest_overall                   	     \
              -gltsym 'SYM: +step30_on +step15_on -rest15_on -rest30_on'   \
              -glt_label 12  step_vs_rest_overall                   	     \
              -gltsym 'SYM: +step30_on +step15_on -stand15_on -stand30_on' \
              -glt_label 13  step_vs_stand_overall                         \
              -gltsym 'SYM: +rest15_on -rest_sham'                         \
              -glt_label 14  rest15_vs_rest_sham                           \
              -gltsym 'SYM: +stand15_on -stand_sham'                       \
              -glt_label 15  stand15_vs_step_sham                          \
              -gltsym 'SYM: +step30_on -step_sham'                         \
              -glt_label 16  step30_vs_step_sham                           \
              -gltsym 'SYM: +stim_on -sham_on'                             \
              -glt_label 17  stim_vs_sham                                  \
              -gltsym 'SYM: +stand_sham -rest_sham'                        \
              -glt_label 18  stand_vs_restSham                             \
              -gltsym 'SYM: +step_sham -rest_sham'                         \
              -glt_label 19  step_vs_restSham                              \
      -regress_est_blur_epits                                              \
      -regress_est_blur_errts                                              \
      -regress_run_clustsim yes




Cheers,
Gerome



Edited 1 time(s). Last edit at 08/02/2019 02:23PM by GMan.
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Subject Author Posted

Choosing the right basis function (old data mystery)

GMan August 02, 2019 02:11PM

Re: Choosing the right basis function (old data mystery)

rick reynolds August 02, 2019 03:55PM

Re: Choosing the right basis function (old data mystery)

GMan August 05, 2019 06:45PM