:orphan: .. _ahelp_3dRetinoPhase: ************* 3dRetinoPhase ************* .. contents:: :local: | .. code-block:: none Usage: 3dRetinoPhase [-prefix ppp] dataset where dataset is a time series from a retinotpy stimulus -exp EXP: These four options specify the type of retinotpy -con CON: stimulus. EXP and CON are for expanding and -clw CLW : contracting rings, respectively. CLW and CCW are -ccw CCW: for clockwise and counter clockwise moving polar polar angle mapping stimuli. You can specify one, or all stimuli in one command. When all are specified polar angle stimuli, and eccentricity stimuli of opposite directions are combined. -prefix PREF: Prefix of output datasets. PREF is suffixed with the following: .ecc+ for positive (expanding) eccentricity (EXP) .ecc- for negative (contracting) eccentricity (CON) .pol+ for clockwise polar angle mapping (CLW) .pol- for counterclockwise polar angle mapping (CCW) At a minimum each input gets a phase dataset output. It contains response phase (or delay) in degrees. If both directions are given for polar and/or eccentricity then a visual field angle data set is created. The visual field angle is obtained by averaging phases of opposite direction stimuli. The hemodynamic offset is half the phase difference. Each output also contains a thresholding sub-brick. Its type depends on the phase estimation method (-phase_estimate). Note on the thresholding sub-bricks ----------------------------------- Both FFT and DELAY values of -phase_estimate produce thresholding sub-bricks with the phase estimates. Those thresholds have associated significance levels, but they should be taken with a grain of salt. There is no correction for autocorrelation, so the DOFs are generous. The program also attaches a thresholding sub-brick to the visual field angle datasets which are estimated by averaging the phase estimates in order to remove the hemodynamic offset. This composite thresholding sub-brick contains at each voxel/node, the maximum threshold from the datasets of stimli of opposite direction. This thresholding sub-brick is for convenience, allowing you to threshold with a mask that is the union of the individual thresholded maps. Significance levels are purposefully not attached. I don't know how to compute them properly. -spectra: Output amplitude and phase spectra datasets. -Tstim T: Period of stimulus in seconds. This parameter does not depend on the number of wedges or rings (Nr/Nw). It is the duration of a full cycle of the stimulus. Use -Tpol TPOL, and -Tecc TECC, to specify periods for each stimulus type separately. -Tstim sets both periods to T. -nrings Nr: Nr is the number of rings in the stimulus. The default is 1. -nwedges Nw: Nw is the number of wedges in the stimulus. The default is 1. -ort_adjust: Number of DOF lost in detrending outside of this program. -pre_stim PRE: Blank period, in seconds, before stimulus began -sum_adjust y/n: Adjust sum of angles for wrapping based on the angle difference. Default is 'y' -phase_estimate METH: Select method of phase estimation METH == FFT uses the phase of the fundamental frequency. METH == DELAY uses the 3ddelay approach for estimating the phase. This requires the use of option -ref_ts . See references [3] and [4] below. The DELAY option appears to be good as the FFT for high SNR and high duty cycle. See results produced by @Proc.PK.All_D in the demo archive AfniRetinoDemo.tgz. However,the DELAY option seems much better for low duty cycle stimuli. It is not set as the default for backward compatibility. Positive and negative feedback about this option are welcome. Thanks to Ikuko Mukai and Masaki Fukunaga for making the case for DELAY's addition; they were right. -ref_ts REF_TS: 0 lag reference time series of response. This is needed for the DELAY phase estimation method. With the DELAY method, the phase results are comparable to what you'd get with the following 3ddelay command: For illustration, say you have stimuli of 32 second periods with the polar stimuli having two wedges. After creating the reference time series with waver (32 sec. block period eccentricity, 32/2=16 sec. block period for polar), run 4 3ddelay commands as such: for an expanding ring of 32 second period: 3ddelay -input exp.niml.dset \ -ideal_file ECC.1D \ -fs 0.5 -T 32 \ -uD -nodsamp \ -phzreverse -phzscale 1.0 \ -prefix ecc+.del.niml.dset\n Repeat for contracting ring, remove -phzreverse for clockwise two wedge of 32 second period: 3ddelay -input clw.niml.dset \ -ideal_file POL.1D \ -fs 0.5 -T 16 \ -uD -nodsamp \ -phzreverse -phzscale 0.5 \ -prefix pol+.del.niml.dset\n Repeat for counterclockwise remove -phzreverse Instead of the 3ddelay mess, all you do is run 3dRetinoPhase with the following extra options: -phase_estimate DELAY -ref_ts ECC.1D or -phase_estimate DELAY -ref_ts POL.1D If you are not familiar with the use of program 'waver' for creating reference time series, take a look at demo script @Proc.PK.All_D in AfniRetinoDemo.tgz. -multi_ref_ts MULTI_REF_TS: Multiple 0 lag reference time series. This allows you to test multiple regressors. The program will run a separate analysis for each regressor (column), and combine the results in the output dataset this way: ([.] denotes output sub-brick) [0]: Phase from regressor that yields the highest correlation coeff. [1]: Maximum correlation coefficient. [2]: Number of regressor that yields the highest correlation coeff. Counting begins at 1 (not 0) [3]: Phase from regressor 1 [4]: Correlation coefficient from regressor 1 [5]: Phase from regressor 2 [6]: Correlation coefficient from regressor 2 ... etc. In general, for regressor k (k starts at 1) [2*k+1] contains the Phase and [2*k+2] the Correlation coefficient N.B: If MULTI_REF_TS has only one timeseries, -multi_ref_ts produces an output identical to that of -ref_ts. See usage in @RetinoProc and demo data in https://afni.nimh.nih.gov/pub/dist/tgz/AfniRetinoDemo.tgz References for this program: [1] RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29: 162-173, 1996. [2] Saad Z.S., et al. SUMA: An Interface For Surface-Based Intra- And Inter-Subject Analysis With AFNI. Proc. 2004 IEEE International Symposium on Biomedical Imaging, 1510-1513 If you use the DELAY method: [3] Saad, Z.S., et al. Analysis and use of FMRI response delays. Hum Brain Mapp, 2001. 13(2): p. 74-93. [4] Saad, Z.S., E.A. DeYoe, and K.M. Ropella, Estimation of FMRI Response Delays. Neuroimage, 2003. 18(2): p. 494-504. ++ Compile date = Apr 18 2024 {AFNI_24.1.03:linux_ubuntu_16_64}