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1. the Brett transform then we recommend that you un Brett the published coordinates using the above transform Brett Talairach to MNI and then proceed with the Lancaster transform MNI SPM to Talairach This will correctly move your coordinates into the Talairach space GingerALE User Manual page 10 4 Help Menu Items Check for Updates This menu item will check the BrainMap website to see if you have the latest version of GingerALE Show Manual This menu item will show the current manual for GingerALE this document An internet connection is necessary for this menu option Show Read Me This menu item will show the current readme file for GingerALE The readme file contains information about installation and version changes An internet connection is necessary for this menu option Show License This menu item will show the current license information for GingerALE An internet connection is necessary for this menu option GingerALE User Manual page 11 References Eickhoff SB Laird AR Grefkes C Wang LE Zilles K Fox PT Coordinate based activation likelihood estimation meta analysis of neuroimaging data A random effects approach based on empirical estimates of spatial uncertainty Hum Brain Mapp 30 2907 2926 2009 Genovese CR Lazar NA Nichols TE Thresholding of statistical maps in functional neuroimaging using the false discovery rate Neuroimage 15 870 878 2002 Laird AR Robinson JL McMil2. BrainMap GingerALE 2 1 http www brainmap org Copyright 2003 2011 Research Imaging Institute UTHSCSA User Manual for GingerALE 2 1 http brainmap org Angela R Laird Ph D Research Imaging Institute UT Health Science Center San Antonio BrainMap Development Team Peter T Fox M D Angela R Laird Ph D Simon B Eickhoff M D Jack L Lancaster Ph D Mick Fox Programmer Analyst Angela M Uecker Programmer Analyst Kimberly L Ray Research Assistant Juan J Saenz Jr Research Assistant Updated 20 May 2011 GingerALE User Manual page 2 About GingerALE GingerALE is used for performing activation or anatomic likelihood estimation ALE meta analyses The ALE meta analysis method was initially developed by Peter Turkeltaub Turkeltaub et al 2002 This method of meta analysis was adopted by BrainMap in 2003 Several modifications have been made to the ALE algorithm since then including those described by Laird et al 2005 The current version of our software is described by Eickhoff et al 2009 with a small modification described by Turkeltaub et al 2011 The full text for these publications is available on www brainmap org pubs New Features in GingerALE e ALE now supports random effect meta analyses rather than fixed effects meta analyses e ALE values are weighted by the sample size of each contributing study e Users now have a choice of running their meta analyses in MNI or Tal
3. GingerALE 3 Tools Menu Items Export Foci Image This menu item creates an nii image of your foci file In this image each coordinate point is assigned a value No blurring of the coordinate points is performed in this export this step is simply intended as a way to view your coordinates in standard space The value assigned to each coordinate point matches the experiment number of your foci file Remember different experiments are defined in a foci file simply by including a line break between the groups of foci By assigning values in this way it is easy to set each experiment number to a different color in your image viewer so that you can identify the paper and experiment for each coordinate point as you scroll through the brain If 2 identical coordinate locations are included in GingerALE User Manual page 9 different experiments then the value assigned to that voxel will be n 1 where n equals the number of total experiments This is done so that these duplicate coordinates can be seen on the resultant output image Convert Foci This menu item uses a dialog window as seen in Fig 5 to guide you through the conversion of your coordinates from MNI space to Talairach space and vice versa You are given options for selecting your input file of coordinates the transform you would like to use and the name and location of your output file There are 8 coordinate transforms included in GingerALE The first three transforms conver
4. airach space e Subtraction analysis is now included for two sets of foci e Streamlined interface that requires fewer buttons Performing ALE Meta Analyses All output files are written in NIfTI nii format The input for a meta analysis in GingerALE is a text file of your foci This file can be generated by hand from an excel worksheet or as an automated export of your workspace in BrainMap Sleuth It is critical that any manually generated file is created with a format that exactly matches what is exported by Sleuth including tags for the number of subjects and the standard brain space e g Talairach or MNI Be sure to include spacing between foci from separate contrasts but not for each individual foci Using non standard formatting in your input foci file can result in empty ALE images If you used Sleuth to create a foci file from your workspace then there is no need to spatially renormalize your MNI coordinates to Talairach space or vice versa This conversion is done automatically when the papers are inserted into the BrainMap database using a transform called icbm2tal developed by Lancaster et al 2007 This new transform provides improved fit over the Brett transform mni2tal and improves the accuracy of meta analyses Laird et al 2010 Please note that we no longer use the Brett transform for conversion of coordinates from MNI space to Talairach space however this transform is included in GingerALE s software to allow
5. doc of cluster analysis on thresholded ALE map In the data history and cluster spreadsheet files the cluster analysis reports a variety of information In the cluster spreadsheet you will see 10 columns of information From left to right these are 1 cluster number 2 volume of cluster in mm 3 5 x y z values of the weighted center of mass of the cluster 6 maximum ALE value observed in the ALE cluster 7 9 x y z values of the location of the maximum ALE value 10 Talairach Daemon anatomical label associated with the location of the maximum ALE value All of this information can be found in both the data history and cluster spreadsheet files The data history file also includes information on the x y z values for the extent of each cluster and reported parameters for different stages of the analysis such as computing the ALE statistic performing the permutation test running FDR and thresholding the ALE map 2 File Menu Items Open Foci Hotkey X F Mac or ctrl F PC This menu item loads in a text file of coordinates into GingerALE The format for this file should be three columns of numbers x y z coordinates separated with tabs or spaces If GingerALE User Manual page 8 you created your foci file in Sleuth the file starts by indicating the standard brain space and subsequent experiments will be separated by a line break and delineated by first author name year and experiment name comments
6. e appropriate parameters are selected for the number of permutations FDR pN value minimum volume extent and output file prefix Then click Compute Subtraction results are processed differently than a simple ALE analysis of a single foci file since it is difficult to interpret the subtraction of two sets of ALE images e g significant areas can have a subtraction value of zero Thus z score images are saved as output for subtraction analyses and the thresholded image and cluster analysis are based on these z score values Citing GingerALE If you use GingerALE in your research please acknowledge our previous work in any resultant publication Eickhoff SB Laird AR Grefkes C Wang LE Zilles K Fox PT Coordinate based activation likelihood estimation meta analysis of neuroimaging data A random effects approach based on empirical estimates of spatial uncertainty Hum Brain Mapp 30 2907 2926 2009 GingerALE User Manual page 5 Laird AR Fox M Price CJ Glahn DC Uecker AM Lancaster JL Turkeltaub PE Kochunov P Fox PT ALE meta analysis Controlling the false discovery rate and performing statistical contrasts Hum Brain Mapp 25 155 164 2005 Turkeltaub PE Eden GF Jones KM Zeffiro TA Meta analysis of the functional neuroanatomy of single word reading Method and validation Neurolmage 16 765 780 2002 Main Menu Items GingerALE File Tools Help Figure 2 The Main Application Menu 1 GingerALE Menu Items Ab
7. ide of this mask The ALE analysis will proceed after this step without any intervention on your part However any coordinates located outside of this mask will not be omitted from subsequent analysis and might possibly yield strange activations on the border of your mask that do not appear to have a center of mass Normally finding coordinates outside of the mask will occur for less than 3 of your total foci we have found this number to be even lower since implementing the Lancaster transform instead of the Brett transform Finding coordinates located outside of the mask is sometimes due to author error e g missing negative sign inverted coordinates etc You can often spot this type of error and correct for it manually For example if a coordinate is listed as being located in the occipital cortex but the given y value is positive and extends outside of the Talairach mask then we recommend that you change the y value from positive to negative before proceeding with ALE Two options are available for your mask size a smaller mask or a larger mask Typically we use the smaller mask for meta analyses of functional imaging studies The larger mask is available for VBM meta analyses because many reported coordinates in these studies are located on the outside of the brain We slightly enlarged the mask for these meta analyses so as to include more foci located at the boundaries of Talairach or MNI space ear mask_diff nii File Edit Vie
8. lan KM Tordesillas Gutierrez D Moran ST Gonzales SM Ray KL Franklin C Glahn DC Fox PT Lancaster JL Comparison of the disparity between Talairach and MNI coordinates in functional neuroimaging data Validation of the Lancaster transform Neuroimage 51 677 683 2010 Laird AR Fox M Price CJ Glahn DC Uecker AM Lancaster JL Turkeltaub PE Kochunov P Fox PT ALE meta analysis Controlling the false discovery rate and performing statistical contrasts Hum Brain Mapp 25 155 164 2005 Lancaster JL Tordesillas Gutierrez D Martinez M Salinas F Evans A Zilles K Mazziotta JC Fox PT Bias between MNI and Talairach coordinates analyzed using the ICBM 152 brain template Hum Brain Mapp 28 1194 1205 2007 Turkeltaub PE Eickhoff SB Laird AR Fox M Wiener M Fox P Minimizing within experiment and within group effects in activation likelihood estimation meta analyses Hum Brain Mapp In Press Turkeltaub PE Eden GF Jones KM Zeffiro TA Meta analysis of the functional neuroanatomy of single word reading Method and validation Neurolmage 16 765 780 2002
9. ld two P value thresholds The RIC generally uses thresholds returned by pN If you prefer pID you can set it as the default thresholding value in the Preferences See Genovese et al 2002 for more details You may also choose if you want the coordinates of any resultant ALE clusters to be reported for all submaxima in a single ALE cluster All extrema or only one coordinate for the maximum ALE statistic in that cluster One extrema Choosing the former option is very useful for large ALE clusters that extend over many different areas of the brain e Output Files Lastly you may specify the output directory for all of your processed ALE files which files you want to output and what your preference is for pop up windows about boundary foci and overwriting files A number of files may be written to output during the ALE procedure We recommend that all of these options be checked ALE Image _ALE nii contains the unthresholded ALE values one computed at every voxel in the brain P Value Image _P nii contains each voxel s P value corrected for multiple comparisons using FDR Thresholded Image _pNO5 nii ALE maps thresholded at a given value this is the final image output Cluster Image _clust nii thresholded ALE map each cluster given an integer value Data History _clust txt reports the analysis parameters and the output of the cluster analysis in text format Cluster Spreadsheet _clust xls excel
10. ompatible with most image viewing software we suggest using Mango to view your meta analysis results www ric uthscsa edu mango For meta analyses performed in Talairach space a Download and open Mango b Open gt Open Image gt select the Talairach template file Colin1 1 nii or the MNI template file Clin27_T1_seg_MNI nii that are available on www brainmap org ale depending on the space in which your meta analysis was performed GingerALE User Manual page 4 c In the brain image that pops up click on File gt Add Overlay gt and select the _pNO5 nii image that you created in the penultimate step of GingerALE This overlays your functional meta analysis results on top of the anatomical template d Click on Edit gt Update Image Range very important e To change the color map go to the smaller rectangular window and click on the red box on the left side move your cursor down to the next red box move to the side text box that pops up move to Color Table then click on your preferred color option Red to Yellow and Spectrum are good for ALE results f Moving your cursor throughout the brain will move you through space Pressing the spacebar will change the orientation of the biggest image axial coronal sagittal g To view anatomical labels of your current location in brain space as well as the coordinates select the button with a graph icon just to the right of the button with a T icon in
11. out GingerALE This menu item contains basic information about GingerALE such as the homepage version number and copyright date Preferences Fig 3 The menu item addresses settings that are relevant to performing ALE meta analyses This information is divided into three sections Mask Options Default Values and Output Files ANO GingerALE Preferences Coordinate Space O Talairach MNI Mask Size More Conservative Smaller O Less Conservative Larger ALE Method Eickhoff HBM 2009 O Turkeltaub Non Additive HBM 2010 FWHM values are subject based Eickhoff 2009 Additional FWHM mm None O False Discovery Rate 0 05 Thresholding Value pn O pID Cluster Min Vol mm 250 Cluster Analysis Peaks All extrema No Sub Maxima Minima 5 Output Directory Change D Desktop Save Output Files for mM ALE Image m Cluster Image m P Value Image m Cluster Spreadsheet M Thresholded Image m Data History Warn me about M Foci Outside Mask C Overwriting Files Figure 3 GingerALE Preferences e Coordinate Space A radio button is available to select which standard space the meta analysis should be performed in Talairach or MNI GingerALE User Manual page 6 Mask Size When a foci file is opened the coordinates are compared against a mask defining the outer limits of Talairach or MNI space A pop up window will appear if any of your coordinates are located outs
12. reconversion of published foci To load your coordinates into GingerALE go to File gt Open Foci Navigate to your desired text file and select If your preferences are set to a standard brain space that does not match the tag in your foci file you will be prompted to change your coordinate system to match A dialog window will inform you if any of your foci are located outside the brain mask typically a small percentage of foci are located outside the mask If a large number of foci are outside the mask please check your foci file for errors The main window of GingerALE will then confirm for you the name of your foci file and the number of coordinates and experiments contained therein Fig 1 The prefix of your foci file will be used when generating output ALE images you may edit this prefix if you choose The ALE meta analysis procedure follows 3 steps First GingerALE computes the ALE values for each voxel in the brain and performs a test to determine the null distribution of the ALE statistic at each voxel We no longer require manually entering the FWHM value as this parameter has been empirically determined Eickhoff et al 2009 Next GingerALE takes the P values from the previous step and computes the threshold for the ALE map using the algorithm from Tom Nichols s website http www sph umich edu nichols FDR Choose a False Discovery Rate q for the desired level of significance e g 0 05 or 0 01 Also choose a minimum cluster
13. size in GingerALE User Manual page 3 mm Lastly GingerALE performs cluster analysis on the thresholded map based on the minimum volume that is specified in the previous step Anatomical labels of final cluster locations are provided by the Talairach Daemon http talairach org O GingerALE Oddball GingerALE Input Data Single Study O Contrast Studies Coordinate System MNI Foci Oddball 2221 Foci 155 Experiments Settings FDR pN 0 05 Min Volume mm 250 Output Files Output Name Prefix Oddball Ready Compute Figure 1 GingerALE Interface To carry out these 3 steps click on Compute and GingerALE will write out a separate image for the unthresholded ALE values corresponding to your foci file the P values at each voxel and a final thresholded ALE map Only voxels that were found to be statistically significant are assigned a value in this map The value that is written out is the computed ALE value The thresholded map is output in nii format and can be read by a number of functional neuroimaging software packages Viewing Your Results Once the thresholded map has been created you ll need an anatomical underlay in order to view the meta analysis results We distribute two templates in Talairach space one general file and one to be used specifically by AFNI and one MNI template on GingerALE s website www brainmap org ale Although our nii files are c
14. t coordinates from MNI space to Talairach space using the Lancaster transform icbm2tal This transform is broken into 3 options based on what software you used for spatial normalization of your data SPM FSL or Other 1 MNI SPM to Talairach 2 MNI FSL to Talairach 3 MNI Other to Talairach The second three transforms perform the corresponding transforms from Talairach space to MNI space using the Lancaster transform Again this transform is broken into 3 software options 4 Talairach to MNI SPM 5 Talairach to MNI FSL 6 Talairach to MNI Other The last 2 transforms are reproductions of the Brett transform mni2tal Two options are given for the Brett transform one for converting from MNI space to Talairach space and the other for converting from Talairach space to MNI space 7 Brett Talairach to MNI 8 Brett MNI to Talairach 000 Convert Foci Input File coords_MNI txt Choose 54 Foci 7 Experiments Choose Transform MNI SPM to Talairach cS Output File coords_Tal txt Choose _ Choose Transform Figure 5 Transforming Coordinates MNI and Talairach Spaces Although the BrainMap database no longer supports use of the Brett transform we feel it is still important that we include it in our software If one of the studies included in your meta analysis generated its coordinates by using SPM for spatial normalization and published those coordinates after conversion using
15. the Mango small window move your cursor down until the globe icon is selected then select your desired anatomical atlas from the dialog window that appears Anatomical labels and coordinates will then appear in top of the small Mango window To get the ALE values for all voxels even ones not found to be significant you ll need to open the file created in the first step of the ALE meta analysis process _ALE nii Subtraction Analysis To compare two different sets of foci and examine them for statistically significant differences in convergence you must first run the separate ALE analyses on the two foci files Then create a combined text file in which foci from both files are merged and run this pooled analysis make sure that experiments that appear in both sets of foci are only reported once in the pooled text file Once the pooled analysis is complete you will need the 3 thresholded ALE files that were create in each of those analyses _pNO5 nii To carry out a subtraction analysis first select the Contrast Studies radio button in the main GingerALE window Open the thresholded ALE image created from the first foci file from the main menu item File gt Open ALE Image 1 Then open the thresholded ALE image created from the second foci file File gt Open ALE Image 2 Then open the thresholded results of the pooled ALE analysis File gt Open Pooled ALE Image Once all of the required data sets are loaded make sure th
16. these descriptors out so that they will not be read by the ALE algorithm Between the commented experiment name and the list of coordinates you should also include a line that details the number of subjects for that group of foci For example your foci text file should look like Reference Talairach Hui 2000 Acupuncture vs Tactile Stimulation Increases Subjects 13 56 15 50 59 18 43 59 21 21 50 18 18 Li 2003 Conventional Acupuncture gt Rest Activations Subjects 20 5 12 82 33 10 8 2 3 77 71 11 37 15 36 62 35 7 64 45 18 15 75 15 54 Li 2003 Electro Acupuncture 2 Hz gt Rest Subjects 20 2 28 77 88 13 15 6 68 35 12 11 56 89 63 43 11 72 49 74 15 21 20 97 Open ALE Image 1 Hotkey g6 1 Mac or ctrl 1 PC Opens an ALE image that corresponds to the first foci file analyzed in a subtraction analysis to test two sets of foci for statistically significant differences Open ALE Image 2 Hotkey 48 2 Mac or ctrl 2 PC Opens an ALE image that corresponds to the second foci file analyzed in a subtraction analysis Open Pooled ALE Image Hotkey 4 3 Mac or ctrl 3 PC Opens an ALE image that corresponds to the first and second foci files merged and analyzed together Save Data History Hotkey S Mac or ctrl S PC This menu item allows you to save a text output that summarizes your ALE meta analysis at any point in the procedure Clear Data This menu item clears your foci from
17. w Analysis ROI Image Plugins Window Figure 4 Difference Between Mask Size Options If you have a large number of outlying foci that you do not want omitted from your meta analysis then you can select the option of Less Conservative Larger This option will slightly increase the default mask size thus including a wider range of coordinates An image of the difference between the two mask files for the Talairach template can be seen in Fig 4 In this difference image the white areas denote the extra voxels included when using the larger less conservative mask file Please note that if you use this larger mask GingerALE User Manual page 7 some of your resultant ALE clusters may appear to be located outside of the brain when viewed on the Talairach or MNI anatomical templates e ALE Method Here you may choose to use the ALE algorithm described by Eickhoff et al 2009 or implement the small correction to minimize within experiment and within group effects described by Turkeltaub et al 2011 In addition since both of these techniques utilize automatically determined FWHM values we provide an option here for advanced users to implement an additional manual FWHM fudge factor Please note that this parameter should be left as None for standard analyses Next you may set default values for the False Discovery Rate pN or pID and minimum cluster volume mm The computation for the false discovery rate will yie
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