:orphan: .. _ahelp_1d_tool.py: ********** 1d_tool.py ********** .. contents:: :local: | 1d_tool.py - for manipulating and evaluating 1D files purpose: ======== .. code-block:: none This program is meant to read/manipulate/write/diagnose 1D datasets. Input can be specified using AFNI sub-brick[]/time{} selectors. examples (very basic for now): ============================== Example 1. Select by rows and columns, akin to 1dcat. ++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Note: columns can be X-matrix labels. 1d_tool.py -infile 'data/X.xmat.1D[0..3]{0..5}' -write t1.1D or using column labels: 1d_tool.py -infile 'data/X.xmat.1D[Run#1Pol#0,,Run#1Pol#3]' \ -write run0_polorts.1D Example 2. Compare with selection by separate options. +++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile data/X.xmat.1D \ -select_cols '0..3' -select_rows '0..5' \ -write t2.1D diff t1.1D t2.1D Example 2b. Select or remove columns by label prefixes. +++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Keep only bandpass columns: 1d_tool.py -infile X.xmat.1D -write X.bandpass.1D \ -label_prefix_keep bandpass Remove only bandpass columns (maybe for 3dRFSC): 1d_tool.py -infile X.xmat.1D -write X.no.bandpass.1D \ -label_prefix_drop bandpass Keep polort columns (start with 'Run') motion shifts ('d') and labels starting with 'a' and 'b'. But drop 'bandpass' columns: 1d_tool.py -infile X.xmat.1D -write X.weird.1D \ -label_prefix_keep Run d a b \ -label_prefix_drop bandpass Example 2c. Select columns by group values, 3 examples. +++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none First be sure of what the group labels represent. 1d_tool.py -infile X.xmat.1D -show_group_labels i) Select polort (group -1) and other baseline (group 0) terms. 1d_tool.py -infile X.xmat.1D -select_groups -1 0 -write baseline.1D ii) Select everything but baseline groups (anything positive). 1d_tool.py -infile X.xmat.1D -select_groups POS -write regs.of.int.1D iii) Reorder to have rests of interest, then motion, then polort. 1d_tool.py -infile X.xmat.1D -select_groups POS 0, -1 -write order.1D iv) Create stim-only X-matrix file: select non-baseline columns of X-matrix and write with header comment. 1d_tool.py -infile X.xmat.1D -select_groups POS \ -write_with_header yes -write X.stim.xmat.1D Or, using a convenience option: 1d_tool.py -infile X.xmat.1D -write_xstim X.stim.xmat.1D Example 2d. Select specific runs from the input. ++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Note that X.xmat.1D may have runs defined automatically, but for an arbitrary input, they may need to be specified via -set_run_lengths. i) .... apparently I forgot to do this... Example 3. Transpose a dataset, akin to 1dtranspose. +++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile t3.1D -transpose -write ttr.1D Example 4a. Zero-pad a single-run 1D file across many runs. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Given a file of regressors (for example) across a single run (run 2), created a new file that is padded with zeros, so that it now spans many (7) runs. Runs are 1-based here. 1d_tool.py -infile ricor_r02.1D -pad_into_many_runs 2 7 \ -write ricor_r02_all.1D Example 4b. Similar to 4a, but specify varying TRs per run. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none The number of runs must match the number of run_lengths parameters. 1d_tool.py -infile ricor_r02.1D -pad_into_many_runs 2 7 \ -set_run_lengths 64 61 67 61 67 61 67 \ -write ricor_r02_all.1D Example 5. Display small details about a 1D dataset: +++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none a. Display number of rows and columns for a 1D dataset. Note: to display them "quietly" (only the numbers), add -verb 0. This is useful for setting a script variable. 1d_tool.py -infile X.xmat.1D -show_rows_cols 1d_tool.py -infile X.xmat.1D -show_rows_cols -verb 0 b. Display indices of regressors of interest from an X-matrix. 1d_tool.py -infile X.xmat.1D -show_indices_interest c. Display X-matrix labels by group. 1d_tool.py -infile X.xmat.1D -show_group_labels d. Display "degree of freedom" information: 1d_tool.py -infile X.xmat.1D -show_df_info e. Display X-matrix stimulus class information (for one class or ALL). 1d_tool.py -infile X.xmat.1D -show_xmat_stim_info aud 1d_tool.py -infile X.xmat.1D -show_xmat_stim_info ALL f. Display X-matrix column index list for those of the given classes. Display regressor labels or in encoded column index format. 1d_tool.py -infile X.xmat.1D -show_xmat_stype_cols AM IM 1d_tool.py -infile X.xmat.1D -show_xmat_stype_cols ALL \ -show_regs_style encoded Example 6a. Show correlation matrix warnings for this matrix. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none This option does not include warnings from baseline regressors, which are common (from polort 0, from similar motion, etc). 1d_tool.py -infile X.xmat.1D -show_cormat_warnings Example 6b. Show entire correlation matrix. ++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile X.xmat.1D -show_cormat Example 6c. Like 6a, but include warnings for baseline regressors. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile X.xmat.1D -show_cormat_warnings_full Example 7a. Output temporal derivative of motion regressors. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none There are 9 runs in dfile_rall.1D, and derivatives are applied per run. 1d_tool.py -infile dfile_rall.1D -set_nruns 9 \ -derivative -write motion.deriv.1D Example 7b. Similar to 7a, but let the run lengths vary. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none The sum of run lengths should equal the number of time points. 1d_tool.py -infile dfile_rall.1D \ -set_run_lengths 64 64 64 64 64 64 64 64 64 \ -derivative -write motion.deriv.rlens.1D Example 7c. Use forward differences. ++++++++++++++++++++++++++++++++++++ .. code-block:: none instead of the default backward differences... 1d_tool.py -infile dfile_rall.1D \ -set_run_lengths 64 64 64 64 64 64 64 64 64 \ -forward_diff -write motion.deriv.rlens.1D Example 8. Verify whether labels show slice-major ordering. This is where all slice0 regressors come first, then all slice1 regressors, etc. Either show the labels and verify visually, or print whether it is true. 1d_tool.py -infile scan_2.slibase.1D'[0..12]' -show_labels 1d_tool.py -infile scan_2.slibase.1D -show_labels 1d_tool.py -infile scan_2.slibase.1D -show_label_ordering Example 9a. Given motion.1D, create an Enorm time series. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Take the derivative (ignoring run breaks) and the Euclidean Norm, and write as e.norm.1D. This might be plotted to show show sudden motion as a single time series. 1d_tool.py -infile motion.1D -set_nruns 9 \ -derivative -collapse_cols euclidean_norm \ -write e.norm.1D Example 9b. Like 9a, but supposing the run lengths vary (still 576 TRs). ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile motion.1D \ -set_run_lengths 64 61 67 61 67 61 67 61 67 \ -derivative -collapse_cols euclidean_norm \ -write e.norm.rlens.1D Example 9c. Like 9b, but weight the rotations as 0.9 mm. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile motion.1D \ -set_run_lengths 64 61 67 61 67 61 67 61 67 \ -derivative -collapse_cols weighted_enorm \ -weight_vec .9 .9 .9 1 1 1 \ -write e.norm.weighted.1D Example 10. Given motion.1D, create censor files to use in 3dDeconvolve. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Here a TR is censored if the derivative values have a Euclidean Norm above 1.2. It is common to also censor each previous TR, as motion may span both (previous because "derivative" is actually a backward difference). The file created by -write_censor can be used with 3dD's -censor option. The file created by -write_CENSORTR can be used with -CENSORTR. They should have the same effect in 3dDeconvolve. The CENSORTR file is more readable, but the censor file is better for plotting against the data. a. general example ~~~~~~~~~~~~~~~~~~ .. code-block:: none 1d_tool.py -infile motion.1D -set_nruns 9 \ -derivative -censor_prev_TR \ -collapse_cols euclidean_norm \ -moderate_mask -1.2 1.2 \ -show_censor_count \ -write_censor subjA_censor.1D \ -write_CENSORTR subjA_CENSORTR.txt b. using -censor_motion ~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: none The -censor_motion option is available, which implies '-derivative', '-collapse_cols euclidean_norm', 'moderate_mask -LIMIT LIMIT', and the prefix for '-write_censor' and '-write_CENSORTR' output files. This option will also result in subjA_enorm.1D being written, which is the euclidean norm of the derivative, before the extreme mask is applied. 1d_tool.py -infile motion.1D -set_nruns 9 \ -show_censor_count \ -censor_motion 1.2 subjA \ -censor_prev_TR c. allow the run lengths to vary ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: none 1d_tool.py -infile motion.1D \ -set_run_lengths 64 61 67 61 67 61 67 61 67 \ -show_censor_count \ -censor_motion 1.2 subjA_rlens \ -censor_prev_TR Consider also '-censor_prev_TR' and '-censor_first_trs'. Example 11. Demean the data. Use motion parameters as an example. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none The demean operation is done per run (default is 1 when 1d_tool.py does not otherwise know). a. across all runs (if runs are not known from input file) 1d_tool.py -infile dfile_rall.1D -demean -write motion.demean.a.1D b. per run, over 9 runs of equal length 1d_tool.py -infile dfile_rall.1D -set_nruns 9 \ -demean -write motion.demean.b.1D c. per run, over 9 runs of varying length 1d_tool.py -infile dfile_rall.1D \ -set_run_lengths 64 61 67 61 67 61 67 61 67 \ -demean -write motion.demean.c.1D Example 12. "Uncensor" the data, zero-padding previously censored TRs. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Note that an X-matrix output by 3dDeconvolve contains censor information in GoodList, which is the list of uncensored TRs. a. if the input dataset has censor information 1d_tool.py -infile X.xmat.1D -censor_fill -write X.uncensored.1D b. if censor information needs to come from a parent 1d_tool.py -infile sum.ideal.1D -censor_fill_parent X.xmat.1D \ -write sum.ideal.uncensored.1D c. if censor information needs to come from a simple 1D time series 1d_tool.py -censor_fill_parent motion_FT_censor.1D \ -infile cdata.1D -write cdata.zeropad.1D Example 13. Show whether the input file is valid as a numeric data file. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none a. as any generic 1D file 1d_tool.py -infile data.txt -looks_like_1D b. as a 1D stim_file, of 3 runs of 64 TRs (TR is irrelevant) 1d_tool.py -infile data.txt -looks_like_1D \ -set_run_lengths 64 64 64 c. as a stim_times file with local times 1d_tool.py -infile data.txt -looks_like_local_times \ -set_run_lengths 64 64 64 -set_tr 2 d. as a 1D or stim_times file with global times 1d_tool.py -infile data.txt -looks_like_global_times \ -set_run_lengths 64 64 64 -set_tr 2 e. report modulation type (amplitude and/or duration) 1d_tool.py -infile data.txt -looks_like_AM f. perform all tests, reporting all errors 1d_tool.py -infile data.txt -looks_like_test_all \ -set_run_lengths 64 64 64 -set_tr 2 Example 14. Split motion parameters across runs. ++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Split, but keep them at the original length so they apply to the same multi-run regression. Each file will be the same as the original for the run it applies to, but zero across all other runs. Note that -split_into_pad_runs takes the output prefix as a parameter. 1d_tool.py -infile motion.1D \ -set_run_lengths 64 64 64 \ -split_into_pad_runs mot.padded The output files are: mot.padded.r01.1D mot.padded.r02.1D mot.padded.r03.1D If the run lengths are the same -set_nruns is shorter... 1d_tool.py -infile motion.1D \ -set_nruns 3 \ -split_into_pad_runs mot.padded Example 15a. Show the maximum pairwise displacement. ++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Show the max pairwise displacement in the motion parameter file. So over all TRs pairs, find the biggest displacement. In one direction it is easy (AP say). If the minimum AP shift is -0.8 and the maximum is 1.5, then the maximum displacement is 2.3 mm. It is less clear in 6-D space, and instead of trying to find an enveloping set of "coordinates", distances between all N choose 2 pairs are evaluated (brute force). 1d_tool.py -infile dfile_rall.1D -show_max_displace Example 15b. Like 15a, but do not include displacement from censored TRs. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile dfile_rall.1D -show_max_displace \ -censor_infile motion_censor.1D Example 15c. Show the entire distance/displacement matrix. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Show all pairwise displacements (vector distances) in a (motion param?) row vector file. Note that the maximum element of this matrix should be the one output by -show_max_displace. 1d_tool.py -infile coords.1D -show_distmat Example 16. Randomize a list of numbers, say, those from 1..40. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none The numbers can come from 1deval, with the result piped to '1d_tool.py -infile stdin -randomize_trs ...'. 1deval -num 40 -expr t+1 | \ 1d_tool.py -infile stdin -randomize_trs -write stdout See also -seed. Example 17. Display min, mean, max, stdev of 1D file. +++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -show_mmms -infile data.1D To be more detailed, get stats for each of x, y, and z directional blur estimates for all subjects. Cat(enate) all of the subject files and pipe that to 1d_tool.py with infile - (meaning stdin). cat subject_results/group.*/sub*/*.results/blur.errts.1D \ | 1d_tool.py -show_mmms -infile - Example 18. Just output censor count for default method. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none This will output nothing but the number of TRs that would be censored, akin to using -censor_motion and -censor_prev_TR. 1d_tool.py -infile dfile_rall.1D -set_nruns 3 -quick_censor_count 0.3 1d_tool.py -infile dfile_rall.1D -set_run_lengths 100 80 120 \ -quick_censor_count 0.3 Example 19. Compute GCOR from some 1D file. +++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none * Note, time should be in the vertical direction of the file (else use -transpose). 1d_tool.py -infile data.1D -show_gcor Or get some GCOR documentation and many values. 1d_tool.py -infile data.1D -show_gcor_doc 1d_tool.py -infile data.1D -show_gcor_all Example 20. Display censored or uncensored TRs lists (for use in 3dTcat). +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none TRs which were censored: 1d_tool.py -infile X.xmat.1D -show_trs_censored encoded TRs which were applied in analysis (those NOT censored): 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded Only those applied in run #2 (1-based). 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded \ -show_trs_run 2 Example 21. Convert to rank order. ++++++++++++++++++++++++++++++++++ .. code-block:: none a. show rank order of slice times from a 1D file 1d_tool.py -infile slice_times.1D -rank -write - b. show rank order of slice times piped directly from 3dinfo 3dinfo -slice_timing epi+orig | 1d_tool.py -infile - -rank -write - c. show rank order using 'competition' rank, instead of default 'dense' 3dinfo -slice_timing epi+orig \ | 1d_tool.py -infile - -rank_style competition -write - Example 22. Guess volreg base index from motion parameters. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile dfile_rall.1D -collapse_cols enorm -show_argmin Example 23. Convert volreg parameters to those suitable for 3dAllineate. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile dfile_rall.1D -volreg2allineate \ -write allin_rall_aff12.1D Example 24. Show TR counts per run. +++++++++++++++++++++++++++++++++++ .. code-block:: none a. list the number of TRs in each run 1d_tool.py -infile X.xmat.1D -show_tr_run_counts trs b. list the number of TRs censored in each run 1d_tool.py -infile X.xmat.1D -show_tr_run_counts trs_cen c. list the number of TRs prior to censoring in each run 1d_tool.py -infile X.xmat.1D -show_tr_run_counts trs_no_cen d. list the fraction of TRs censored per run 1d_tool.py -infile X.xmat.1D -show_tr_run_counts frac_cen e. list the fraction of TRs censored in run 3 1d_tool.py -infile X.xmat.1D -show_tr_run_counts frac_cen \ -show_trs_run 3 Example 25. Show number of runs. ++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -infile X.xmat.1D -show_num_runs Example 26. Convert global index to run and TR index. +++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Note that run indices are 1-based, while TR indices are 0-based, as usual. Confusion is key. a. explicitly, given run lengths 1d_tool.py -set_run_lengths 100 80 120 -index_to_run_tr 217 b. implicitly, given an X-matrix (** be careful about censoring **) 1d_tool.py -infile X.nocensor.xmat.1D -index_to_run_tr 217 Example 27. Display length of response curve. +++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none 1d_tool.py -show_trs_to_zero -infile data.1D Print out the length of the input (in TRs, say) until the data values become a constant zero. Zeros that are followed by non-zero values are irrelevant. Example 28. Convert slice order to slice times. +++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none A slice order might be the sequence in which slices were acquired. For example, with 33 slices, perhaps the order is: set slice_order = ( 0 6 12 18 24 30 1 7 13 19 25 31 2 8 14 20 \ 26 32 3 9 15 21 27 4 10 16 22 28 5 11 17 23 29 ) Put this in a file: echo $slice_order > slice_order.1D 1d_tool.py -set_tr 2 -slice_order_to_times \ -infile slice_order.1D -write slice_times.1D Or as a filter: echo $slice_order | 1d_tool.py -set_tr 2 -slice_order_to_times \ -infile - -write - Example 29. Display minimum cluster size from 3dClustSim output. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Given a text file output by 3dClustSim, e.g. ClustSim.ACF.NN1_1sided.1D, and given both an uncorrected (pthr) and a corrected (alpha) p-value, look up the entry that specifies the minimum cluster size needed for corrected p-value significance. If requested in afni_proc.py, they are under files_ClustSim. a. with modestly verbose output (default is -verb 1) 1d_tool.py -infile ClustSim.ACF.NN1_1sided.1D -csim_show_clustsize b. quiet, to see just the output value 1d_tool.py -infile ClustSim.ACF.NN1_1sided.1D -csim_show_clustsize \ -verb 0 c. quiet, and capture the output value (tcsh syntax) set clustsize = `1d_tool.py -infile ClustSim.ACF.NN1_1sided.1D \ -csim_show_clustsize -verb 0` Example 30. Display columns that are all-zero (e.g. censored out) +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none Given a regression matrix, list columns that are entirely zero, such as those for which there were no events, or those for which event responses were censored out. a. basic output Show the number of such columns and a list of labels 1d_tool.py -show_regs allzero -infile zerocols.X.xmat.1D b. quiet output (do not include the number of such columns) 1d_tool.py -show_regs allzero -infile zerocols.X.xmat.1D -verb 0 c. quiet encoded index list 1d_tool.py -show_regs allzero -infile zerocols.X.xmat.1D \ -show_regs_style encoded -verb 0 d. list all labels of regressors of interest (with no initial count) 1d_tool.py -show_regs set -infile zerocols.X.xmat.1D \ -select_groups POS -verb 0 command-line options: ===================== basic informational options: ++++++++++++++++++++++++++++ .. code-block:: none -help : show this help -hist : show the module history -show_valid_opts : show all valid options -ver : show the version number required input: +++++++++++++++ .. code-block:: none -infile DATASET.1D : specify input 1D file general options: ++++++++++++++++ .. code-block:: none -add_cols NEW_DSET.1D : extend dset to include these columns -backward_diff : take derivative as first backward difference Take the backward differences at each time point. For each index > 0, value[index] = value[index] - value[index-1], and value[0] = 0. This option is identical to -derivative. See also -forward_diff, -derivative, -set_nruns, -set_run_lens. -collapse_cols METHOD : collapse multiple columns into one, where METHOD is one of: min, max, minabs, maxabs, euclidean_norm, weighted_enorm. Consideration of the euclidean_norm method: For censoring, the euclidean_norm method is used (sqrt(sum squares)). This combines rotations (in degrees) with shifts (in mm) as if they had the same weight. Note that assuming rotations are about the center of mass (which should produce a minimum average distance), then the average arc length (averaged over the brain mask) of a voxel rotated by 1 degree (about the CM) is the following (for the given datasets): TT_N27+tlrc: 0.967 mm (average radius = 55.43 mm) MNIa_caez_N27+tlrc: 1.042 mm (average radius = 59.69 mm) MNI_avg152T1+tlrc: 1.088 mm (average radius = 62.32 mm) The point of these numbers is to suggest that equating degrees and mm should be fine. The average distance caused by a 1 degree rotation is very close to 1 mm (in an adult human). * 'enorm' is short for 'euclidean_norm'. * Use of weighted_enorm requires the -weight_vec option. e.g. -collapse_cols weighted_enorm -weight_vec .9 .9 .9 1 1 1 -censor_motion LIMIT PREFIX : create censor files This option implies '-derivative', '-collapse_cols euclidean_norm', 'moderate_mask -LIMIT LIMIT' and applies PREFIX for '-write_censor' and '-write_CENSORTR' output files. It also outputs the derivative of the euclidean norm, before the limit it applied. The temporal derivative is taken with run breaks applied (derivative of the first run of a TR is 0), then the columns are collapsed into one via each TR's vector length (Euclidean Norm: sqrt(sum of squares)). After that, a mask time series is made from TRs with values outside (-LIMIT,LIMIT), i.e. if >= LIMIT or <= LIMIT, result is 1. This binary time series is then written out in -CENSORTR format, with the moderate TRs written in -censor format (either can be applied in 3dDeconvolve). The output files will be named PREFIX_censor.1D, PREFIX_CENSORTR.txt and PREFIX_enorm.1D (e.g. subj123_censor.1D, subj123_CENSORTR.txt and subj123_enorm.1D). Besides an input motion file (-infile), the number of runs is needed (-set_nruns or -set_run_lengths). Consider also '-censor_prev_TR' and '-censor_first_trs'. See example 10. -censor_fill : expand data, filling censored TRs with zeros -censor_fill_parent PARENT : similar, but get censor info from a parent The output of these operation is a longer dataset. Each TR that had previously been censored is re-inserted as a zero. The purpose of this is to make 1D time series data properly align with the all_runs dataset, for example. Otherwise, the ideal 1D data might have missing TRs, and so will align worse with responses over the duration of all runs (it might start aligned, but drift earlier and earlier as more TRs are censored). See example 12. -censor_infile CENSOR_FILE : apply censoring to -infile dataset This removes TRs from the -infile dataset where the CENSOR_FILE is 0. The censor file is akin to what is used with "3dDeconvolve -censor", where TRs with 1 are kept and those with 0 are excluded from analysis. See example 15b. -censor_first_trs N : when censoring motion, also censor the first N TRs of each run -censor_next_TR : for each censored TR, also censor next one (probably for use with -forward_diff) -censor_prev_TR : for each censored TR, also censor previous -cormat_cutoff CUTOFF : set cutoff for cormat warnings (in [0,1]) -csim_show_clustsize : for 3dClustSim input, show min clust size Given a 3dClustSim table output (e.g. ClustSim.ACF.NN1_1sided.1D), along with uncorrected (pthr) and corrected (alpha) p-values, show the minimum cluster size to achieve significance. The pthr and alpha values can be controlled via the options -csim_pthr and -csim_alpha (with defaults of 0.001 and 0.05, respectively). The -verb option can be used to provide additional or no details about the clustering method. See Example 29, along with options -csim_pthr, -csim_alpha and -verb. -csim_pthr THRESH : specify uncorrected threshold for csim output e.g. -csim_pthr 0.0001 This option implies -csim_show_clustsize, and is used to specify the uncorrected p-value of the 3dClustSim output. See also -csim_show_clustsize. -csim_alpha THRESH : specify corrected threshold for csim output e.g. -csim_alpha 0.01 This option implies -csim_show_clustsize, and is used to specify the corrected, cluster-wise p-value of the 3dClustSim output. See also -csim_show_clustsize. -demean : demean each run (new mean of each run = 0.0) -derivative : take the temporal derivative of each vector (done as first backward difference) Take the backward differences at each time point. For each index > 0, value[index] = value[index] - value[index-1], and value[0] = 0. This option is identical to -backward_diff. See also -backward_diff, -forward_diff, -set_nruns, -set_run_lens. -extreme_mask MIN MAX : make mask of extreme values Convert to a 0/1 mask, where 1 means the given value is extreme (outside the (MIN, MAX) range), and 0 means otherwise. This is the opposite of -moderate_mask (not exactly, both are inclusive). Note: values = MIN or MAX will be in both extreme and moderate masks. Note: this was originally described incorrectly in the help. -forward_diff : take first forward difference of each vector Take the first forward differences at each time point. For index0: regressors of interest This option can be used to select columns by integer groups, with special cases of POS (regs of interest), NEG (probably polort). Note that NONNEG is unneeded as it is the pair POS 0. See also -show_group_labels. -select_cols SELECTOR : apply AFNI column selectors, [] is optional e.g. '[5,0,7..21(2)]' -select_rows SELECTOR : apply AFNI row selectors, {} is optional e.g. '{5,0,7..21(2)}' -select_runs r1 r2 ... : extract the given runs from the dataset (these are 1-based run indices) e.g. 2 e.g. 2 3 1 1 1 1 1 4 -set_nruns NRUNS : treat the input data as if it has nruns (e.g. applies to -derivative and -demean) See examples 7a, 10a and b, and 14. -set_run_lengths N1 N2 ... : treat as if data has run lengths N1, N2, etc. (applies to -derivative, for example) Notes: o option -set_nruns is not allowed with -set_run_lengths o the sum of run lengths must equal NT See examples 7b, 10c and 14. -set_tr TR : set the TR (in seconds) for the data -show_argmin : display the index of min arg (of first column) -show_censor_count : display the total number of censored TRs Note : if input is a valid xmat.1D dataset, then the count will come from the header. Otherwise the input is assumed to be a binary censor file, and zeros are simply counted. -show_cormat : display correlation matrix -show_cormat_warnings : display correlation matrix warnings (this does not include baseline terms) -show_cormat_warnings_full : display correlation matrix warnings (this DOES include baseline terms) -show_distmat : display distance matrix Expect input as one coordinate vector per row. Output NROWxNROW matrix of vector distances. See Example 15c. -show_df_info : display info about degrees of freedom (found in in xmat.1D formatted files) -show_df_protect yes/no : protection flag (def=yes) -show_gcor : display GCOR: the average correlation -show_gcor_all : display many ways of computing (a) GCOR -show_gcor_doc : display descriptions of those ways -show_group_labels : display group and label, per column -show_indices_baseline : display column indices for baseline -show_indices_motion : display column indices for motion regressors -show_indices_interest : display column indices for regs of interest -show_label_ordering : display the labels -show_labels : display the labels -show_max_displace : display max displacement (from motion params) - the maximum pairwise distance (enorm) -show_mmms : display min, mean, max, stdev of columns -show_num_runs : display number of runs found -show_regs PROPERTY : display regressors with the given property Show column indices or labels for those columns where PROPERTY holds: allzero : the entire column is exactly 0 set : (NOT allzero) the column has some set (non-zero) value How the columns are displayed is controlled by -show_regs_style (label, encoded, comma, space) and -verb (0, 1 or 2). With -verb > 0, the number of matching columns is also output. See also -show_regs_style, -verb. See example 30. -show_regs_style STYLE : use STYLE for how to -show_regs This only applies when using -show_regs, and specifies the style for how to show matching columns. space : show indices as a space-separated list comma : show indices as a comma-separated list encoded : succinct selector list (like sub-brick selectors) label : if xmat.1D has them, show space separated labels set : (NOT allzero) the column has some set (non-zero) value How the columns are displayed is controlled by -show_regs_style (label, encoded, comma, space) and -verb (0, 1 or 2). -show_rows_cols : display the number of rows and columns -show_tr_run_counts STYLE : display TR counts per run, according to STYLE STYLE can be one of: trs : TR counts trs_cen : censored TR counts trs_no_cen : TR counts, as if no censoring frac_cen : fractions of TRs censored See example 24. -show_trs_censored STYLE : display a list of TRs which were censored -show_trs_uncensored STYLE : display a list of TRs which were not censored STYLE can be one of: comma : comma delimited space : space delimited encoded : succinct selector list verbose : chatty See example 20. -show_trs_run RUN : restrict -show_trs_[un]censored to the given 1-based run -show_trs_to_zero : display number of TRs before final zero value (e.g. length of response curve) -show_xmat_stype_cols T1 ... : display columns of the given class types Display the columns (labels, indices or encoded) of the given stimulus types. These types refer specifically to those with basis functions, and correspond with 3dDeconvolve -stim_* options as follows: times : -stim_times AM : -stim_times_AM1 or -stim_times_AM2 AM1 : -stim_times_AM1 AM2 : -stim_times_AM2 IM : -stim_times_IM Multiple types can be provided. See example 5f. See also -show_regs_style. -show_xmat_stim_info CLASS : display information for the given stim class (CLASS can be a specific one, or 'ALL') Display information for a specific (3dDeconvolve -stim_*) stim class. This includes the class Name, the 3dDeconvolve Option, the basis Function, and the relevant Columns of the X-matrix. See example 5e. See also -show_regs_style. -show_group_labels : display group and label, per column -slice_order_to_times : convert a list of slice indices to times Programs like to3d, 3drefit, 3dTcat and 3dTshift expect slice timing to be a list of slice times over the sequential slices. But in some cases, people have an ordered list of slices. So the sorting needs to change. If TR=2 and the slice order is: 0 2 4 6 8 1 3 5 7 9 Then the slices/times ordered by time (as input) are: slices: 0 2 4 6 8 1 3 5 7 9 times: 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 And the slices/times ordered instead by slice index are: slices: 0 1 2 3 4 5 6 7 8 9 times: 0.0 1.0 0.2 1.2 0.4 1.4 0.6 1.6 0.8 1.8 It is this final list of times that is output. See example 28. -sort : sort data over time (smallest to largest) - sorts EVERY vector - consider the -reverse option -split_into_pad_runs PREFIX : split input into one padded file per run e.g. -split_into_pad_runs motion.pad This option is used for breaking a set of regressors up by run. The output would be one file per run, where each file is the same as the input for the run it corresponds to, and is padded with 0 across all other runs. Assuming the 300 row input dataset spans 3 100-TR runs, then there would be 3 output datasets created, each still be 300 rows: motion.pad.r01.1D : 100 rows as input, 200 rows of 0 motion.pad.r02.1D : 100 rows of 0, 100 rows as input, 100 of 0 motion.pad.r03.1D : 200 rows of 0, 100 rows as input This option requires either -set_nruns or -set_run_lengths. See example 14. -transpose : transpose the input matrix (rows for columns) -transpose_write : transpose the output matrix before writing -volreg2allineate : convert 3dvolreg parameters to 3dAllineate This option should be used when the -infile file is a 6 column file of motion parameters (roll, pitch, yaw, dS, dL, dP). The output would be converted to a 12 parameter file, suitable for input to 3dAllineate via the -1Dparam_apply option. volreg: roll, pitch, yaw, dS, dL, dP 3dAllinate: -dL, -dP, -dS, roll, pitch, yaw, 0,0,0, 0,0,0 These parameters would be to correct the motion, akin to what 3dvolreg did (i.e. they are the negative estimates of how the subject moved). See example 23. -write FILE : write the current 1D data to FILE -write_sep SEP : use SEP for column separators -write_style STYLE : write using one of the given styles basic: the default, don't work too hard ljust: left-justified columns of the same width rjust: right-justified columns of the same width tsv: tab-separated (use as in -write_sep '\t') -weight_vec v1 v2 ... : supply weighting vector e.g. -weight_vec 0.9 0.9 0.9 1 1 1 This vector currently works only with the weighted_enorm method for the -collapse_cols option. If supplied (as with the example), it will weight the angles at 0.9 times the weights of the shifts in the motion parameters output by 3dvolreg. See also -collapse_cols. -write_censor FILE : write as boolean censor.1D e.g. -write_censor subjA_censor.1D This file can be given to 3dDeconvolve to censor TRs with excessive motion, applied with the -censor option. e.g. 3dDeconvolve -censor subjA_censor.1D This file works well for plotting against the data, where the 0 entries are removed from the regression of 3dDeconvolve. Alternatively, the file created with -write_CENSORTR is probably more human readable. -write_CENSORTR FILE : write censor times as CENSORTR string e.g. -write_CENSORTR subjA_CENSORTR.txt This file can be given to 3dDeconvolve to censor TRs with excessive motion, applied with the -CENSORTR option. e.g. 3dDeconvolve -CENSORTR `cat subjA_CENSORTR.txt` Which might expand to: 3dDeconvolve -CENSORTR '1:16..19,44 3:28 4:19,37..39' Note that the -CENSORTR option requires the text on the command line. This file is in the easily readable format applied with -CENSORTR. It has the same effect on 3dDeconvolve as the sister file from -write_censor, above. -verb LEVEL : set the verbosity level R Reynolds March 2009