This file lists some details on the options that can be selected and the numbers assigned to plots. ----------------------------------------------------------- VAMCA OPTIONS: You can pass in a command string to "vamca" to control its output. All you have to do is to cut and paste one of the following strings into the command "vamca(' ')" inbetween the single quotes: file1=''inputMNI.txt''; % to change the input filename This mandatory input should be the name of a text file containing a 3D coordinate on each line as the first 3 numbers and an optional 4th number as a coordinate weight. One can also specify the type of normalization applicable to each coordinate from the following choices: TAL - Talairach coordinate (default) MNI - generic MNI coordinate MNISPM - MNI coordinate computed by SPM MNIFSL - MNI coordinate computed By FSL TALSPM - Talairach coordinate computed by converting an SPM normalized brain to MNI space and then applying the Brett MNItoTAL transform. TALFSL - Ditto, but using FSL for the MNI normalization TALMNI - Ditto, but with some other MNI normalization It is also possible when doing an ROI analysis to specify ROIs directly as activations in the following format: mni rh 1 15 0.0833 mni lh 2 9 0.0769 The first specifies that L1 type ROI #15 (medialorbitalfrontal) in the right hemisphere was activated and has weight 0.0833 assigned to it. The second specifies that L2 type ROI #9 (Triangular part of the inferior frontal gyrus) in the left hemisphere was activated (weight 0.0769). See areaRestrictL1 and areaRestrictL2 for codes. Finally, any text after the '%' symbol is treated as an unprocessed comment file2=''inputMNI2.txt''; % to change the comparison group filename An optional input to use as a comparison group. If file2=file1, then the two hemispheres are compared to each other when processing the right hemisphere's coordinates. fileout=''outputMNI''; % to change the output '.txt' and '.img' filenames Name of the text and image files that are output containing some of the results of the analysis: fileout.txt - contains details of the converted 3D coordinates, corresponding surface locations, permutation tests, and impacted ROIs. fileout.img - ANALYZE format file containing 3D MNI coordinates: The values for 3D coordinates in these files is +1 for file1 coordinates, -1 for file2 coordinates. This file can be overlayed on anatomical and DTI atlas images processed from the subject database found in the "Images" directory. extraPoints=''none.txt''; % extra points to plot along with color and shape An optional text file of 3D points that are plotted in the "contour" plot along with color/size description replacing the 4th 'weight' number. Color and size information is represented as a number of the form RGB.S, where R, G, and B are each a digit from 0-9 indicating how much Red, Green, and Blue color to combine to color the square, and S (0-9) specifies how large the plotted square should be. See V1V2VPV3.txt for an example of plots of visual cortex points. permSurf=1; % = 0 to turn off surface permutation test Specifies whether (1) or not (0) to perform the surface permutation test that checks to see if the distance between the two group (file1 and file2) medians is unusually large. If so, it indicates that the two groups, on average, have activations in different areas on the cortical surface. See VAMCAmethod.pdf for more info on the test. permSurfDisp=0; % = 1 to turn on the surface permutation dispersion test Specifies whether (1) or not (0) to perform the surface permutation dispersion test as an adjunct to the above test. A low p value obtained from this test indicates that the two groups (file1 vs file2) being analyzed have significantly diffferent location dispersions. If so this can mean that a moderately low p value (e.g. p=0.05) in the permSurf test might be explained by this heterogeneous dispersion. perm3D=1; % = 0 to turn off 3D permutation test Specifies whether (1) or not (0) to perform the MNI space permutation test that checks to see if the distance between the two group (file1 and file2) medians is unusually large. If so, it indicates that the two groups, on average, have activations in different areas in MNI space. See VAMCAmethod.pdf for more info on the test. A 3D dispersion test (analogous to that in permSurfDisp) is performed. scatterSurf=1; % = 0 to turn off display of individual surface scatter Specifies whether (1) or not (0) to plot the scatter of cortical surface points associated with each MNI coordinate. One plot for each 3D coordinate is displayed. figureAdd=0; % = X to add X to all figure numbers (useful if you % want to compare surface maps from 2 different runs) Add this value to every figure number for all plots. This can be used when doing multiple VAMCA runs to compare plots from different analyses. A multiple of 10000 is good to use. mw=''MW1''; % = Mollweide view (default auditory) Which surface view of the cortical surface to use: 'MW1' - Mollweide 1 - auditory cortex 'MW2' - Mollweide 2 - auditory/visual/motor cortices 'MW3' - Mollweide 3 - motor/sensory/association cortices 'MW4' - Mollweide 4 - visual cortex See vamca.html to look at their layouts. mwSurface=''''; % = Mollweide surface tag This could be useful in the event that cortical surfaces other than of mid-gray-matter (e.g. pial surface) are ever released. Right now it doesn't do anything. print3D=''MNI''; % = print out 3D coordinates in MNI or TAL space Choose to print out all coordinates in 'fileout.txt' as 'MNI' or 'TAL' coordinates. np=5000; % = Y to change the number of permutations in the group test Specify the number of permutations to use in all of the permutation tests. sdmax=5; % = distance from surface considered irrelevant to computing surface medians The maximal distance (in mm) to look in order to identify the closest surface point to a given 3D point (for a given database subject). This can be related to the average or maximal thickness of a cortex, indicating how far activations can be away from an individual's cortex (for purposes of reconstructing the activations cortical location). mtsmax=sdmax*0.8; % = the maximum allowable mean distance from a point to database surfaces The maximal mean 3D distance (in mm) over all database subjects from a coordinate to the cortical surfaces in order that the coordinate be used/displayed by VAMCA. hemax=sdmax/2; % = distance across midline to use points This variable allows one to control how far across the midline VAMCA can look when processing points that are associated with a given hemisphere. The two hemispheres are considered separately, so it is possible for a coordinate near the midline to be assigned to both hemispheres. One can adjust this variable to test whether medial surface coordinates are being double counted or conversely to make sure mean cortical petalia is not being incorrectly discounted. ppumin=0.2; % = proportion of database subjects required to have a surface within sdmax This variable allows one to screen out coordinates that are not close enough to the surfaces of a minimum number of database cortices. E.g. the default is that 20% of VAMCA database's subjects must have cortical surfaces within 5mm of a coordinate for the coordinate to be used. normals=''Right.txt''; % = altas of normals to use (right handed only default) List of database subjects to use: All.txt - 72 subjects Right.txt - 60 right handed subjects Left.txt - 12 left handed subjects Male.txt - 39 male subjects Female.txt - 33 female subjects RM.txt - 33 male right handed subjects RF.txt - 6 male left handed subjects LM.txt - 27 female right handed subjects LF.txt - 6 femeale left handed subjects These text files contain age information in case you want to make a new list of database subjects to use from a certain age range. There are also average cortical surface files to use if you need to process your data very quickly (lose a little accuracy) or if you have a lot of data to process. Median.txt - A Median cortical surface defined from "Right.txt" Mean.txt - A Mean cortical surface defined from "Right.txt" VectorMedian.txt - A Vector Median surface defined from "Right.txt" Averages.txt - Use all 3 of the above average cortical surfaces ccont=0.33; % = brightness of gyri in contour plots (0-1) cback=0; % = brightness of sulci in contour plots (0-ccont) copaq=0; % = opaqueness of contour colors (0-ccont)(0=transparent) cext=1; % = size of MNI points on contour plots (=0,1,2,3, small to large) sext=2; % = ditto for aggregate surface map points cmext=1; % = size of MNI median points on contour plots (=0,1,2,3, small to large) smext=2; % = ditto for aggregate surface map median points maxconext=99; % = maximum contour extent in pixels The above are just here so that you can adjust how the plots look: the 'ext' ones adjust the size of crosses in plots. areaRestrictL1=0; % extract only point in these L1 surface zones Specify whether or not (0) you wish to restrict processing 3D coordinates to those included in certain ROIs or lobes. This value can be set to a matlab-compatible vector of numbers corresponding to FreeSurfer L1 ROI parcellation, or the name of a lobe: ''Frontal'' ''Occipital'' ''Parietal'' ''Temporal'' ''Cingulate'' 1 for unknown 2 for bankssts 3 for caudalanteriorcingulate 4 for caudalmiddlefrontal 5 for corpuscallosum 6 for cuneus 7 for entorhinal 8 for fusiform 9 for inferiorparietal 10 for inferiortemporal 11 for isthmuscingulate 12 for lateraloccipital 13 for lateralorbitofrontal 14 for lingual 15 for medialorbitofrontal 16 for middletemporal 17 for parahippocampal 18 for paracentral 19 for parsopercularis 20 for parsorbitalis 21 for parstriangularis 22 for pericalcarine 23 for postcentral 24 for posteriorcingulate 25 for precentral 26 for precuneus 27 for rostralanteriorcingulate 28 for rostralmiddlefrontal 29 for superiorfrontal 30 for superiorparietal 31 for superiortemporal 32 for supramarginal 33 for frontalpole 34 for temporalpole 35 for transversetemporal This parcellation of the cortical surface is coarser than the L2 parcellation, but is more compatible with dividing up the surface into lobes. See Fischl et al, Automatically Parcellating the Human Cerebral Cortex, Cerebral Cortex, 14:11-22, 2004. areaRestrictL2=0; % extract only point in these L2 surface zones Specify whether or not (0) you wish to restrict processing 3D coordinates to those included in certain ROIs or lobes. This value can be set to a matlab-compatible vector of numbers corresponding to FreeSurfer L2 ROI parcellation, or the name of a lobe: ''Frontal'' ''Occipital'' ''Parietal'' ''Temporal'' ''Cingulate'' ''Insula'' 1 for Unknown 2 for Corpus_callosum 3 for G_and_S_Insula_ONLY_AVERAGE 4 for G_cingulate-Isthmus 5 for G_cingulate-Main_part 6 for G_cuneus 7 for G_frontal_inf-Opercular_part 8 for G_frontal_inf-Orbital_part 9 for G_frontal_inf-Triangular_part 10 for G_frontal_middle 11 for G_frontal_superior 12 for G_frontomarginal 13 for G_insular_long 14 for G_insular_short 15 for G_and_S_occipital_inferior 16 for G_occipital_middle 17 for G_occipital_superior 18 for G_occipit-temp_lat-Or_fusiform 19 for G_occipit-temp_med-Lingual_part 20 for G_occipit-temp_med-Parahippocampal_part 21 for G_orbital 22 for G_paracentral 23 for G_parietal_inferior-Angular_part 24 for G_parietal_inferior-Supramarginal_part 25 for G_parietal_superior 26 for G_postcentral 27 for G_precentral 28 for G_precuneus 29 for G_rectus 30 for G_subcallosal 31 for G_subcentral 32 for G_temporal_inferior 33 for G_temporal_middle 34 for G_temp_sup-G_temp_transv_and_interm_S 35 for G_temp_sup-Lateral_aspect 36 for G_temp_sup-Planum_polare 37 for G_temp_sup-Planum_tempolare 38 for G_and_S_transverse_frontopolar 39 for Lat_Fissure-ant_sgt-ramus_horizontal 40 for Lat_Fissure-ant_sgt-ramus_vertical 41 for Lat_Fissure-post_sgt 42 for Medial_wall 43 for Pole_occipital 44 for Pole_temporal 45 for S_calcarine 46 for S_central 47 for S_central_insula 48 for S_cingulate-Main_part_and_Intracingulate 49 for S_cingulate-Marginalis_part 50 for S_circular_insula_anterior 51 for S_circular_insula_inferior 52 for S_circular_insula_superior 53 for S_collateral_transverse_ant 54 for S_collateral_transverse_post 55 for S_frontal_inferior 56 for S_frontal_middle 57 for S_frontal_superior 58 for S_frontomarginal 59 for S_intermedius_primus-Jensen 60 for S_intraparietal-and_Parietal_transverse 61 for S_occipital_anterior 62 for S_occipital_middle_and_Lunatus 63 for S_occipital_superior_and_transversalis 64 for S_occipito-temporal_lateral 65 for S_occipito-temporal_medial_and_S_Lingual 66 for S_orbital-H_shapped 67 for S_orbital_lateral 68 for S_orbital_medial-Or_olfactory 69 for S_paracentral 70 for S_parieto_occipital 71 for S_pericallosal 72 for S_postcentral 73 for S_precentral-Inferior-part 74 for S_precentral-Superior-part 75 for S_subcentral_ant 76 for S_subcentral_post 77 for S_suborbital 78 for S_subparietal 79 for S_supracingulate 80 for S_temporal_inferior 81 for S_temporal_superior 82 for S_temporal_transverse This parcellation of the cortical surface is finer than the L1 parcellation, and divides up the cortical surface into gyri and sulci (S for sulcus and G for gyrus above). See Fischl et al, Automatically Parcellating the Human Cerebral Cortex, Cerebral Cortex, 14:11-22, 2004 and Destrieux et al, Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature, Neuroimage, 53: 1-15, 2010. drawL1=0; % draw the L1 boundaries on the basic plots Specifies whether or not (0) to outline L1 ROIs on the plots of surface coordinates. A value of "1" will plot all of the L1 ROIs specified by the areaRestrictL1 parameter value (all if this is 0) whereas a vector of integers in [1,35] will outline the corresponding ROIs (see areaRestrictL1 above). drawL2=0; % draw the L2 boundaries on the basic plots Specifies whether or not (0) to outline L2 ROIs on the plots of surface coordinates. A value of "1" will plot all of the L2 ROIs specified by the areaRestrictL2 parameter value (all if this is 0) whereas a vector of integers in [1,82] will outline the corresponding ROIs (see areaRestrictL2 above). permL1=0; % do the surface ROI permutation for the L1 parcellation (coarser) Specify whether (1) or not (0) to perform the ROI foci density permutation tests over the L1 ROI parcellations specified by areaRestrictL1 (all of them if none specified). The output for these tests appear in 'fileout.txt' and are plotted as histograms showing the results for the density test and the density difference test. See VAMCAmethod.pdf for some info on the test. permL2=0; % do the surface ROI permutation for the L2 parcellation (gyral/sulcal) Specify whether (1) or not (0) to perform the ROI foci density permutation tests over the L2 ROI parcellations specified by areaRestrictL2 (all of them if none specified). The output for these tests appear in 'fileout.txt' and are plotted as histograms showing the results for the density test and the density difference test. See VAMCAmethod.pdf for some info on the test. balanceLxWeights=1; % balance weights when used in ROI permutation test Instructs VAMCA to balance coordinate weights across groups when doing an ROI permutation test. This is useful when the number of coordinates or total weight in each group is unbalanced, but might best be turned off when doing a "pureROIanalysis". Balancing the weights allows the smaller group's weights to be competitive in an ROI density difference permutation test. pureROIanalysis=0; % use even weights in impinged ROIs per study Performs an indicator-stle ROI permutation significance analysis (Etkins and Wager, J Am Psychiatry 164: 10 2007). This analysis looks to see whether or not a study has some coordinates within an ROI and then assigns the study's weight (sqrt(# of subjects)) to that ROI for that study. Multiple coordinates within the ROI do not increase the chance of significance. numNullStudies1=0; % number of studies in group 1 (=file1) that found no activations numNullStudies2=0; % number of studies in group 2 (=file2) that found no activations These options allow one to specify the number of studies that found no significant activations at all - useful when doing an ROI permutation test in that circumstance or if checking a result's robustness to the "file drawer" effect (unpublished negative results). numNullWeights1=0; % weights for null studies for group 1 numNullWeights2=0; % weights for null studies for group 2 One specifies the total study weight assigned to each of the above completely negative results. If 0, the square root of the mean of the number of subjects in each positive study is used. ----------------------------------------------------------- VAMCA PLOT NUMBERS: 1,2,3,.... Numbers assigned to plots showing individual cortical anatomy locations for each subject in the database corresponding to a single 3D coordinate when using the scatterSurf=1 option. 1000 The plots showing the results of the 3D group centroid distance permutation test (left hemisphere) performed by setting perm3D=1. 1001 The plots showing the results of the 3D group centroid distance permutation test (right hemisphere) performed by setting perm3D=1. 1005 Basic plot of median surface points, one for each 3D coordinate, (both hemispheres) including ROI outlines (if selected using drawL1 or drawL2) for group 1 (file1). 1006 Basic plot of median surface points, one for each 3D coordinate, (both hemispheres) including ROI outlines (if selected using drawL1 or drawL2) for group 2 (file2). 1010 The plots showing the results of the surface group centroid distance permutation test (left hemisphere) performed by setting permSurf=1. Also includes the surface dispersion test chosen using permSurfDisp=1; 1011 The plots showing the results of the 3D group centroid distance permutation test (right hemisphere) performed by setting permSurf=1. Also includes the surface dispersion test chosen using permSurfDisp=1; 1015 Contour plot showing both group 1 (file1) and group 2's (file2) surface points together along with ROI outlines (as in 1005 and 1006) plus, if any permutation tests were chosen (perm3D=1 or permSurf=1), a contour cloud background indicating the two groups locations (red for group 1, blue for group 2, and purple when they are in the same location, on average). 1016 Multifiducial plots defined using the postprocesing command 1017 "vamcaPlot(inputfile1);" 1020 Plots of the surface density permutation test results in each ROI chosen using areaRestrictL1 or areaRestrictL2 for each such ROI containing some surface foci (left hemisphere). 1021 Plots of the surface density permutation test results in each ROI chosen using areaRestrictL1 or areaRestrictL2 for each such ROI containing some surface foci (left hemisphere). 1030 Beta version of left hemisphere 3D rendered mean cortical surface view of plot 1015 (only available for MW2 view) 1032 Beta version of right hemisphere 3D rendered mean cortical surface view of plot 1015 (only available for MW2 view)