:orphan: .. _ahelp_@chauffeur_afni: *************** @chauffeur_afni *************** .. contents:: :local: | OVERVIEW ======== .. code-block:: none This was originally a helper function in processing scripts, to take quality control (QC) snapshots automatically. It wraps around a lot (but not all) of the veeery useful "driving AFNI" functionality. You, dear user, can still accomplish all the same with those commands, but I just wanted to add in some other calculations, as well, to try to make the process of generating montages of images easier. The purpose of this function is to generate montage images easily and quickly while processing-- even if on a remote server (because it uses xvfb to make a virtual X11 environment)-- to be able to see what is happening in data processing at useful stages: for example, alignment of two sets without having to click any buttons in the AFNI GUI. This makes it easier to review batch processing, discuss processing with one's boss, prepare for a presentation or publication, etc. For example, this program is used in most all of FATCAT's fat_proc_* scripts, and even TORTOISE includes calls to it for auto-QC imaging if the user has AFNI installed (and suuuurely they should??). Each call to this function will make a set of montages in the axial, coronal and sagittal planes, of user-specified dimensionality. This function can be used on both 3D and 4D data sets, but for the latter, probably @djunct_4d_imager would be much more simple to use. A lot of the help descriptions for command line options, below, will refer to the variables in the "AFNI Driver" doc: https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.driver.html or variables in the "AFNI Environment" doc: https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html References to these are sometimes noted explicitely with "see DR" or "see ENV", respectively, and potentially with the particular variable. For example, "(see ENV: SAVE_AGIF)". Added ~July 15, 2018: the capability to select a single slice across a 4D data set and to view it with both underlay and overlay options (hitherto, @djunct_4d_imager had a subset of this capability but only for ulays). ++ constructed by PA Taylor (NIMH, NIH, USA). # ========================================================================= COMMAND OPTIONS =============== .. code-block:: none -help, -h :see helpfile (here, in fact) -hview :popup help -ver :see version number -ulay UUU :name of underlay dset (required); can be 3D or 4D set, depending on the circumstances. For 4D, though, strongly consider using "@djunct_4d_imager". -olay OOO :name of overlay dset (opt). -mode_4D :for each viewing plane (sag, cor, axi) one slice is selected across all volumes in a 4D data set (e.g., using one of the "-set_* .." opts, below). A montage of those slices is made for any ulay UUU and olay OOO selected. Note that with this option: + the user cannot thresold by statistic with the "-thr_olay_p2stat .." opt (-> because different stats in a volume might have different conversions) + when using this opt, at least on of UUU and OOO *must* have >1 volumes. + if one of the ulay/olay volumes has only one brick, it will be viewed in the same way across the entire montage (i.e., as if it were a constant volume throughout 'time'). -olay_off :explicitly state you are not using olay (opt); if not used and no olay is given, then the user just gets prompted to be sure they haven't forgotten the olay dset. -prefix PPP :prefix for output files (required). -ulay_range UMIN UMAX :specify min and max range values of ulay dset; if a "%" is on both numbers, then treat the numerical part of UMIN and UMAX as percentiles from which to calculate actual values; otherwise, treat UMIN and UMAX as values directly. (def: UMIN=0% and UMAX=98%). (See DR: SET_ULAY_RANGE) Also, see "Special Ulay Range" and "Combining %ile values..." in NOTES, below. -ulay_range_nz UMIN UMAX :same as the preceding opt, but when "%" is on both numbers, here the percentiles are only calculated over the *non-zero* voxels. The above one is more in line with the AFNI GUI default behavior for percentile calcs (though GUI by default works slicewise). If %ile values are not given, then both this and the above option produce identical results for the same UMIN and UMAX values. (See DR: SET_ULAY_RANGE) "Special Ulay Range" and "Combining %ile values..." in NOTES, below. -ulay_range_am UMIN UMAX :same as the preceding opt, but over just *automasked* voxels -ulay_min_fac UMF :a finesse-full option for further adjusting ulay grayscale mapping, when applying '-ulay_range_am ..'. UMF must be a numerical value in range (0, 1]. This value is used to lower the lower end of the ulay range (UMIN) by this fraction of the difference between the upper and lower bounds. Thus, if A and B are the min and max, respectively, for the ulay, then A -> max(0, A-UMF*(B-A)). -edgy_ulay :turn the ulay volume into edges (via 3dedge3). All other opt/values like the '-ulay_range*' will refer to this edge-ified version, *except* for the '-box_focus_slices AMASK_FOCUS_ULAY' one, whereby the original ulay will still be automasked. If using this option, extensive testing has found that '-ulay_range_nz 0% 50%' or thereabouts might be a nice scale for the brightness. -edge_enhance_ulay EE :a related (but different) way to enhance edges of the ulay than '-edgy_ulay': first, calculate edges, yes, but then use those to scale up the values in the ulay set *at* edge locations. The ulay set value at edges will be multiplied by '1+EE' (one plus the edge enhancement factor). A good value to try using is probably EE=0.5 (and yes, you always need to provide that EE value). -globalrange GR :specify how lookup range for matching ulay values is done (def: VOLUME); (see ENV: AFNI_IMAGE_GLOBALRANGE) Ignored if '-ulay_range* ..' is set. Note for '-mode_4D': this setting applies to the resliced volume (i.e., the one made of one slice of each subbrick). See "Combining %ile values..." in NOTES, below. -func_range FR :specify upper value FR of the olay dset to be matched to top of colorbar (def: calc 98%ile non-zero value of dset and use that). -func_range_perc_nz FRP :alternative to "-func_range ..."; specify a percentile value FRP to use to make the upper value of the olay dset to be matched to the top of the colorbar (def: calc 98%ile non-zero value of dset and use that). NB: this percentile range is always among *non-zero* voxel values with this option; see below. -func_range_perc FRP :same as above option, but this is a percentile among *all* voxel values, not just those with non-zero values (def: 100). -func_range_perc_am FRP :same as above option, but this is a percentile among *automasked* voxel values. -obliquify OBL :the ulay and/or the olay may have been acquired with oblique coordinate axes; by default, the viewer shows these data sets in each of their oblique coordinates. You can choose to apply the obliquity information to show the data in different coords, though, via the value of OBL: "ALL" : apply the obliquity of all entered dsets (via '3dWarp -deoblique ...') to show each in scanner coords "o2u" : send the olay to the ulay's oblique coords "ob2u": send the olay and any box_focus to the ulay's oblique coords "u2o" : send the ulay to the olay's oblique coords "ub2o": send the ulay and any box_focus to the olay's oblique coords -obl_resam_ulay OIU :if using '-obliquity ..', then you might want to specify the method of resampling/interpolation for the dset being re-gridded; this option specifies that method for the ulay (see below for other dsets). Any valid transform opt for 3dWarp is allowed: cubic, NN, etc. (def: OIU = wsinc5) -obl_resam_olay OIO :same as for '-obl_interp_ulay ..', but for the olay dset (def: OIO = wsinc5) -obl_resam_box OIB :same as for '-obl_interp_ulay ..', but for the '-box_focus_slices ..' dset (def: OIB = wsinc5) -func_resam RES :set the resampling mode for dsets; valid values are: NN Li Cu Bk (def: NN; hey, voxels are voxels). (See DR: SET_FUNC_RESAM) -thr_olay THR :threshold the olay dset at THR (def: 0, or unthreshold). If you are thresholding a statistic brick, then you should see the "-thr_olay_p2stat ..." option, below. (See DR: SET_THRESHNEW) -thrflag 'fff' :further control of how the THR value is interpreted (def: "*"). (See DR: SET_THRESHNEW) -thr_olay_p2stat PP :an alternative way to specify a voxelwise threshold (i.e., instead of "-thr_olay ..."), when thresholding based on a statistic; you can specify the p-value you want, and using internal header information, the appropriate value for whatever statistic is in the statistic brick will be calculated and applied; you likely need to use "-set_subbricks i j k" with this, where 'k' would be the index of the statistic brick (and likely 'j' would be the index of the associated coefficient/beta brick; 'i' would be the brick of the underlay volume, and if there is only a single volume there, it could just be either '0' or '-1'). And see next option '-thr_olay_pside', below. -thr_olay_pside SS :(required if using '-thr_olay_p2stat ..') specify the sidedness of the testing for the conversion of p-to-stat. Valid values for SS at present include: bisided 2sided 1sided -cbar CCC :specify a new colorbar, where CCC can be any of the cbars in the standard AFNI list (def: Plasma). -colorscale_idx_file CI CF :another way to specify a colorbar, in this case one created by the user. Two arguments must be input. First, CI is a colorscale index, which must be in the (inclusive) range [01, 99], using two numbers. (The user has to enter this, because they might have one/more of these specified already in their ~/.afnirc file, and hence avoid duplicating an index.) Second, CF is the colorscale filename; the file contains the name of the colorbar in the first line, and then either 2 columns (values and colors) or 1 column (just colors; will be evenly spaced). An example CF is: Yellow-Lime-Red-Blue 1.0 #ffff00 0.7 limegreen 0.5 #ff0000 0.3 #aa00aa 0.0 #0000ff Note the types of AFNI-allowed colornames used here (hex and specific colorname). (see ENV: AFNI_COLORSCALE_xx) -pbar_posonly :for color range specification, default is to use both positive and negative values; enter this flag to use only the positive range. (See DR: SET_PBAR_ALL) -pbar_saveim PBS :if an olay is used, then you can save the color pbar (=colorbar) that is used in plotting. PBS is the name of the file (including path), with allowed extensions jpg, png, or ppm (def: jpg). When this option is used, a text file of the same name as PBS but with extension 'txt' will also be saved, which is now (>May 8, 2019) a dictionary-like file of relevant information: min/max range, threshold value (0, if no thr is specified), as well as the ability to store comments on what those values mean (see -pbar_comm_* options, below). See also '-pbar_dim ..' for relation pbar optioning. (See DR: PBAR_SAVEIM) -pbar_comm_range PBR :if using '-pbar_saveim ..', one can save a text/string comment on why the pbar range was chosen. For example, '99%ile in mask'. This will be output in the PBS.txt file (the value of the key 'pbar_comm'). Use quotes around on command line. -ulay_comm UC :if using '-pbar_saveim ..', one can save a text/string comment on why the ulay range was chosen. For example, '0-25% in volume'. This will be output in the PBS.txt file (the value of the key 'ulay_comm'). Use quotes around on command line. -pbar_comm_thr PBT :similar to '-pbar_comm_range ..', but for storing a comment about the selected threshold value. It will also be stored in the PBS.txt file (the value of the key 'vthr_comm'). -pbar_comm_gen PBG :similar to '-pbar_comm_range ..', but for storing a general comment about the pbar or plot or color range. It will also be stored in the PBS.txt file (the value of the key 'gen_comm'). -pbar_for PF :tiny option, mainly for APQC purposes. In the output txt file of info for the pbar, can state if the pbar refers to something other than the 'olay' (such as the 'ulay' or 'dset'). (def: olay) -pbar_dim PBD :if '-pbar_saveim ..' is used to save the color pbar of the olay, then this option can specify the orientation of the colorbar image and its pixel dimensions. This is done by specifying the 'dimstring' part of the PBAR_SAVEIM input (see DR: PBAR_SAVEIM). The default value is '64x512H', which means to have a vertical cbar that is 64 pixels wide and 512 pixels tall which is then tipped horizontally on its side; to leave it vertical just don't put an 'H' at the end. -XXXnpane P :same option as in 'afni', for colorbar control: << set the number of 'panes' in the continuous colorscale to the value 'P', where P is an even integer between 256 and 2048 (inclusive). Probably will work best if P is an integral multiple of 256 (e.g., 256, 512, 1024, 2048). [This option is for the mysterious Dr ZXu.] >> One use of this option: for ROI atlases with integer values >255. -cbar_ncolors NC :set colorscale mode (def: 99) (See DR: SET_PBAR_ALL, the 2nd usage case, description about '99'). -cbar_topval TOPV :set colorscale mode (def: 1) (See DR: SET_PBAR_ALL, the 2nd usage case, description about 'topval'). Now, the value of TOPV could also be a special keyword, 'EMPTY' (yes, written in all caps), which gives the same behavior as making TOPV the empty "", but makes scripting easier (not needing to pass double quotes in shell variables...). This is probably only useful if defining a discrete colorbar (see Examples). -opacity OO :enter an "opacity factor" for the olay, where OO is an integer in the interval [0, 9], with the 9 being opaque (see DR). -blowup BB :enter a "blowup factor", where BB is an integer in the interval [1, 8]. Increases spatial resolution in the output by a factor of BB (see DR; def: 2). -set_xhairs XX :specify type and/or existence of crosshairs in the image (see DR: SET_XHAIRS). -set_xhair_gap GG :specify gap in the crosshairs to the specified number of pixels GG (see DR: SET_XHAIR_GAP). -delta_slices DS DC DA :when montaging, (DS, DC, DA) is the integer number of slices to use as spacing between views along the (sag, cor, axi) axes, respectively (def: automatically calculate to ~evenly fit the number of selected montage slices along this axis). (See DR: "mont=PxQ:R"; basically, each D? is the 'R' value along the given axis). Users can specify a delta_slice value along *some* axis and leave other(s) to be chosen automatically, by specifying a D? value >0 for their own value, and given any other D? value -1. For example: -delta_slices 40 -1 -1 would specify every 40th slice along the sag axis, while the cor and axi spacing would be automatically calculated. -set_subbricks i j k :for 3D image viewing, specify subbricks being viewed in the ulay, olay and threshold dsets (def: "-1 -1 -1", which means ignore these values). This is the way to specify different overlay and threshold subbricks for displaying, such as using the "beta" or "coefficient" for color and the "statistic" as the threshold level. (See DR: SET_SUBBRICKS) -save_ftype FTYPE :type of file as which to save images; key types are listed in the Driver description (def: PNG) (See DR: SAVE_ALLJPEG, SAVE_ALLPNG, SAVE_MPEG, SAVE_AGIF, SAVE_JPEG, SAVE_PNG; for which the user would enter just the non-"SAVE_" part, just as "PNG", "MPEG", etc.) -set_ijk II JJ KK :Set the controller coordinates to the given triple, which are integer index selectors along the three spatial axes. This essentially specifies the middle image in the montage (def: for each coordinate, choose middle slice along axis). -set_dicom_xyz XX YY ZZ :Set the controller coordinates to the given triple, which are the (x, y, z) coordinates in AFNI's favorite RAI DICOM notation. (def: for each coordinate, choose middle slice along axis). -box_focus_slices REF :Use a dset REF to define a narrow range of where slices cover. This is done by autoboxing the REF dset (with '3dAutobox -noclust', so if it hasn't been masked already, it's not useful), and using the midpoint of the box's FOV as the new center; also, the montage slices are chosen to be evenly spread within the box FOV, though they *still* show the unboxed dataset. This is different than cropping (see '-crop*' below for that); this is only to try to avoid showing empty slices and such. If the ulay is a template dset, you might make REF that template. Just for '3D' dset viewing NEW: enter a keyword for the argument REF, instructing the program to make a focus box from the ulay or olay: AMASK_FOCUS_ULAY or AMASK_FOCUS_OLAY, respectively. Mask is just made using default 3dAutomask (with '-clfrac 0.2', to err on the side of inclusivity)-- may not be perfect, but provide some useful focus while hopefully not cutting off regions that should still be included. NB: if your olay dset is a mask and you want to use it for this box-focusing, then make REF be the name of the file itself, not AMASK_FOCUS_OLAY, because automasking a mask does weird things. -clusterize "-opt0 v0 -opt1 v1 ..." :input a set of options "-opt0 v0 -opt1 v1 ..." for 3dClusterize to use internally, so that the overlay dataset is clusterized. Can be combined with Alpha+Boxed. See the "Clusterize capabilities" description in the NOTES below for what options go where when clusterizing. Examples are also included below. -clust_wami CW :if using '-clusterize ..', then this option can be used to run AFNI's whereami program on the results. The user provides the name of an allowed atlas for reference (see the top of whereami's help), and a text file reporting the relative overlap of each ROI will be produced in the outputs. -montx MX :in creating a montage, the number of image panels in a row, i.e., the number of columns (def: 3); the total number of panels per axis is: MX*MY (see below "-monty ..."). (See DR: "mont=PxQ:R"; basically, MX is the 'P' value). -monty MY :in creating a montage, the number of image panels in a column, i.e., the number of rows (def: 3); the total number of panels per axis is: MX*MY (see above "-montx ..."). (See DR: "mont=PxQ:R"; basically, MY is the 'Q' value). -montgap MG :in creating a montage, one can put a border (or "gap") between the image panels. This is specified as a number of pixels with which to insert between images (def: 0). (See DR: "mont=PxQ:R" additional option ":G:C"; basically, MG is the 'G' value). -montcolor MC :in creating a montage, one can put a border (or "gap") between the image panels (see "-montgap", above); one can also specify a color for this gap, using the present option (def: 'black'). (See DR: "mont=PxQ:R" additional option ":G:C"; basically, MC is the 'C' value). -button_press BP :simulate a button press for one of the following buttons in an image viewer window: Norm Colr Swap You can enter more than one of these button presses here *if* you put all of them within a single pair of quotes, such as: -button_press "Colr Swap". Note that the order of the button presses matters. (See DR: "butpress=name") -no_cor :no coronal slice views output (def: this view is shown) -no_axi :no axial slice views output (def: this view is shown) -no_sag :no sagittal slice views output (def: this view is shown) NB: when '-mode_4D' is on, the sagittal view will ALWAYS shown; effectively, this opt is then disabled. -olay_alpha {No|Yes|Linear|Quadratic} :In addition to representing olay values as colors with a threshold, one also apply opacity information to 'soften' the effect of thresholding; see DR: SET_FUNC_ALPHA for a description of this behavior (def: "No", which is just standard thresholding stuff). Prodigal functionality returned: one can now specify whether fading is "Quadratic" (= "Yes", too, since this is default fading) or "Linear": that is, how quickly opacity drops off, with the former being much faster. At present, a possible rule of thumb: try Quadratic for individual results and Linear for group results. -olay_boxed {No|Yes} :a partner parameter for the fancy alpha-based olay viewing; put a box around supra-threshold voxels/clusters. Default value is "No". (see DR: SET_FUNC_BOXED) -image_zoom_nn_no :the default zoom is set to NN mode, so no smoothing occurs (see ENV: AFNI_IMAGE_ZOOM_NN). This option changes behavior internally to set this variable to have the value "NO". -agif_delay AD :when using "-save_ftype AGIF", this option can be used to specify the time delay between frames. Units are "centi-seconds" = 100ths of seconds (def: 30). (see ENV: AFNI_AGIF_DELAY) -left_is_left LIL :specify explicitly whether image left is dataset left (LIL -> YES) or image left is dataset right (LIL -> NO) (def: no value given). (see ENV: AFNI_LEFT_IS_LEFT) -left_is_posterior LIP :specify explicitly whether image left is dataset posterior (LIP -> YES) or image left is dataset anterior (LIP -> NO) (def: no value given). (see ENV: AFNI_LEFT_IS_POSTERIOR) -crop_axi_x CAX1 CAX2, -crop_axi_y CAY1 CAY2 :crop axial image(s) to be between voxels CAX1 and CAX2 along the x-axis (inclusive) and CAY1 and CAY2 along the y-axis. These values are integer row and column numbers. (See DR: "crop=x1:x2,y1:y2"; CAX1 is x1, etc.; def: no cropping -- CAX1=0, CAX2=0, etc.) -crop_sag_x CSX1 CSX2, -crop_sag_y CSY1 CSY2 :same as other '-crop_*' above, but for sagittal images. -crop_cor_x CCX1 CCX2, -crop_cor_y CCY1 CCY2 :same as other '-crop_*' above, but for coronal images. -zerocolor ZC :Change the default 'background' ulay color of zero values (def: "Black"); ZC can be set to any allowed AFNI value (see ENV: AFNI_IMAGE_ZEROCOLOR). This option is mainly for G. Chen, who flaunts convention whenever possible. -label_mode LM :control labels, ON/OFF and location (def: 1); (see ENV: AFNI_IMAGE_LABEL_MODE) -label_size LS :control labels, size (def: 3); (see ENV: AFNI_IMAGE_LABEL_SIZE) -label_color LC :control labels, color (def: white); (see ENV: AFNI_IMAGE_LABEL_COLOR) -label_setback LB :control labels, offset from edge (def: 0.01); (see ENV: AFNI_IMAGE_LABEL_SETBACK) -label_string LSTR :control labels, string automatically appended to the slice (def: ""); (see ENV: AFNI_IMAGE_LABEL_STRING) -image_label_ijk :If this option is used, then the image label will be based on the slice index rather than the spatial (mm) coordinate; thanks, Bob. (see ENV: AFNI_IMAGE_LABEL_IJK) -pass :does nothing (no, really). -no_clean :by default, the temporary directory of copying files and such is now (as of July 8, 2018) removed; using this option means that that working directory should *not* be removed. -do_clean :Use this option to remove the temporary directory of copied/intermediate files. (As of July 8, 2019, this is the new default behavior. Thus, this opt is only here for backwards compatability). -echo :run script verbosely (with 'set echo' executed) # ======================================================================== NOTES ===== Description of "4D mode" ++++++++++++++++++++++++ .. code-block:: none In this case the assumption/requirement is that you have at least one 4D data set to look at; for each viewing plane, one slice is selected across time for viewing. For each viewing plane, the slices across time are spatially concatenated to form a single, temporary 3D dset (a "planar" or "slicewise" volume), which is what is actually put into AFNI to generate images in that relevant plane. How percentile values are calculated is discussed in the next "NOTE", below. When both an overlay and underlay are used, the usual resampling rules of the AFNI GUI apply (and user can specify the resampling option with "-func_resam .."). If one volume is 4D and one is 3D (e.g., for checking alignment across time), then the relevant single slice of the 3D volume is basically just repeated in a given plane. Combining %ile values "-mode_4D" for olay and/or ulay +++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none When using a percentile to set a range in 4D mode for either ulay (e.g., "-ulay_range* ..") or olay (e.g., "-func_range_perc_nz* .."), that percentile is calculated for each of the three "planar" or "slicewise" volumes, and then the *max* of those three numbers is applied with the colorbar. If one of your ulay or olay in 4D mode is just a 3D volume and you want a percentile related to the whole thing, you can calculate any of those values beforehand using "3dBrickStat -percentile ..", and then apply those. Special Ulay Range ++++++++++++++++++ .. code-block:: none If UMAX is a percentile >100%, then what happens is this: the 98%ile value in the dset is calculated, and the result is multiplied by (UMAX/98); the ulay dataset is 'ceilinged' at the 98%ile value, and its upper range is set to UMAX/98. The purpose of this madness? To give a nice, controllably darkened ulay (esp. when that is an anatomical). My suspicion is that having a darker-than-usual ulay is nice to allow the overlay colors to show up better. I am currently of the opinion that a UMAX of around ~150-190% is a nice value (and UMIN can be set to 0%) Clusterize capabilities (with alpha+boxed) ++++++++++++++++++++++++++++++++++++++++++ .. code-block:: none It is now possible to include both Clusterizing and the Alpha+Boxed functionality from the GUI in @chauffeur_afni. A few rules for using this: + There is a new '-clusterize ..' option, where users would put 3dClusterize options for the clustering (e.g., '-NN ..' and '-clust_nvox ..'). But not *everything goes here; in fact, most other cluster-necessary information is provided through existing @chauffeur_afni options, listed below. - Put the utilized Clusterize options in quotes, so it will be read in as a single opt. + The Olay and Thr volumes (for visualizing and thresholding, respectively) are specified with the '-set_subbricks ..' (instead of including '-idat ..' and '-ithr ..' via '-clusterize ..'). + The threshold value is specified with either '-thr_olay ..' or '-thr_olay_pside ..' (instead of including it after sidedness via '-clusterize ..'). 3dClusterize's 'within_range' functionality cannot be used here. - 1sided thresholding is only to the right side. - If the user selects "1sided" thresholding, then '-pbar_posonly' will automatically be switched on. + Sidedness must *always* be included, using '-thr_olay_pside ..', even if not converting a p-value. + The Clusterize report is output in the same place as the final images, as PREFIX_clust_rep.txt. The ability to run 'whereami' on the output clusters is also now included, via the '-clusterize_wami ..' option. This leads to a report of the overlap of each cluster in the cluster map with the specified atlas. The output text file of information is then: PREFIX_clust_whereami.txt. There are a couple examples of using this functionality, below, in EXAMPLES. # ======================================================================== TROUBLESHOOTING =============== .. code-block:: none 1) Sometimes, people running this program (or others that use it) might see an error involving "/tmp/.X11-unix", such as: -- trying to start Xvfb :570 [1] 53344 _XSERVTransmkdir: ERROR: euid != 0,directory /tmp/.X11-unix will not be created. _XSERVTransSocketUNIXCreateListener: mkdir(/tmp/.X11-unix) failed, errno = 2 _XSERVTransMakeAllCOTSServerListeners: failed to create listener for local (EE) Fatal server error: (EE) Cannot establish any listening sockets - Make sure an X server isn't already running(EE) The following has appears to be a good solution (NB: it does require having administrative or sudo privileges): mkdir /tmp/.X11-unix sudo chmod 1777 /tmp/.X11-unix sudo chown root /tmp/.X11-unix/ This is described more here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html#troubleshooting # ======================================================================== EXAMPLES ======== .. code-block:: none A) Basic vanilla: make a 3x5 montage of just a ulay; there will be 15 slices shown, evenly spaced along each axis, with some labels on the corners. @chauffeur_afni \ -ulay MY_ULAY.nii.gz \ -prefix PRETTY_PICTURE \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 4 \ -do_clean B) Make a 3x5 montage of an overlayed data set that has an ROI map, so we want it to be colored-by-integer. Put the images into a pre-existing directory, SUBDIR/. @chauffeur_afni \ -ulay MY_ULAY.nii.gz \ -olay MY_OLAY.nii.gz \ -pbar_posonly \ -cbar "ROI_i256" \ -func_range 256 \ -opacity 4 \ -prefix SUBDIR/PRETTY_PICTURE2 \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 4 \ -do_clean C) Make a 3x5 montage of an overlayed data set that shows the beta coefficients stored in brick [1] while thresholding the associated statistic stored in brick [2] at voxelwise p=0.001, overlayed on the anatomical volume. @chauffeur_afni \ -ulay anat.nii.gz \ -olay stats.nii.gz \ -cbar Plasma \ -func_range 3 \ -thr_olay_p2stat 0.001 \ -thr_olay_pside bisided \ -set_subbricks -1 1 2 \ -opacity 4 \ -prefix STAT_MAP \ -montx 5 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 4 \ -do_clean D) Fun way to enter a colorbar-- note all the '-cbar*' options working together here, and the way they are used to make a discrete cbar. (You might also enjoy the '-colorscale_idx_file ..' option, as another way to enter your own colorbar; colors entered there are *not* discrete regions, but get blended together.) NB 1: now you can replace the "" with the keyword EMPTY, to make scripting easier (needing to keep quotes around can be a pain). NB 2: the string following cbar probably can*not* be split into multiple lines with continuation-of-line chars. Mi dispiace. @chauffeur_afni \ -ulay FT_anat+orig. \ -olay FT_anat+orig. \ -func_range_perc 95 \ -prefix AAA \ -pbar_saveim BBB.jpg \ -pbar_posonly \ -cbar_ncolors 6 \ -cbar_topval "" \ -cbar "1000=yellow 800=cyan 600=rbgyr20_10 400=rbgyr20_08 200=rbgyr20_05 100=rbgyr20_03 0=none" E) Included Clusterizing, with Alpha+Boxed on. Also select the Olay (idat) and Thr (ithr) volumes descriptively, with subbrick labels. @chauffeur_afni \ -ulay anat.nii.gz \ -olay stats.nii.gz \ -cbar Reds_and_Blues_Inv \ -clusterize "-NN 1 -clust_nvox 157" \ -func_range 3 \ -set_subbricks -1 "vis#0_Coef" "vis#0_Tstat" \ -thr_olay_p2stat 0.001 \ -thr_olay_pside bisided \ -olay_alpha Yes \ -olay_boxed Yes \ -opacity 7 \ -prefix img_e \ -montx 3 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 4 \ -no_clean F) Included Clusterizing, with Alpha+Boxed on, similar to above, but 1sided example, and using 'whereami' functionality: @chauffeur_afni \ -pbar_posonly \ -ulay anat.nii.gz \ -olay stats.nii.gz \ -cbar "Spectrum:yellow_to_red" \ -clusterize "-NN 1 -clust_nvox 157" \ -clusterize_wami "MNI_Glasser_HCP_v1.0" \ -func_range 3 \ -set_subbricks -1 1 2 \ -thr_olay 3.314300 \ -thr_olay_pside 1sided \ -olay_alpha Yes \ -olay_boxed Yes \ -opacity 7 \ -prefix img_f \ -montx 3 -monty 3 \ -set_xhairs OFF \ -label_mode 1 -label_size 4 \ -no_clean # -------------------------------------------------------------------