User Manual for GingerALE 2.3
Contents
1. Eickhoff SB Bzdoc D Laird AR Roski C Caspers S Zilles K Fox PT Co activation patters distinguish cortical modules their connectivity and functional differentiation Neuroimage 57 938 949 2011 Laird AR Robinson JL McMillan 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 Robinson JL Laird AR Glahn DC Lovallo WR Fox PT Metaanalytic connectivity modeling Delineating the functional connectivity of the human amygdala Hum Brain Mapp 31 173 184 2010 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 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 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 Laird AR Fox M Glahn DE Fox PT Automated analys2. 7 64 45 18 15 75 15 54 be in a comment which starts with Be sure to include an empty line between foci in separate Geleet Li 2003 Electro Acupuncture 2 Hz gt Rest groups but not between each individual focus i Subjects 20 within the same group 2 28 77 88 13 15 6 68 35 12 11 Since implementing the variable uncertainty of 56 89 63 43 11 72 the random effects method in Eickhoff et al 49 74 15 21 20 97 2009 GingerALE needs subject information for Figure 1 Example foci data each foci group to calculate Fig 2 the Full Width Half Maximum FWHM of the Gaussian function used to blur the foci Larger subject sizes get a tighter taller Gaussian If any foci groups are missing subject information GingerALE will show a warning dialog after loading the foci file The analysis can continue assuming a subject size of 1 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 GingerALE User Manual page 4 Subjects FWHM mm Subject to FWHM 1 19 07 19 2 14 74 S 3 12 98 o 4 12 00 16 5 11 37 15 6 10 94 W 10 10 00 15 9 50 5 11 28 9 01 i 50 8 75 195 8 50 8 Infinity 8 41 Ww Figure 2 Subject size versus Full Width Half Maxi
3. Experiments 32376 mm the voxel wise minimum value of the input ALE images Pooled Data Sets LR insula ALE pNO1 Two ALE contrast images are created by directly subtracting one input image from the other This ALE subtraction image does not take into account differences between the studies To correct for study FDR pN E one sizes Eickhoff et al 2011 GingerALE creates simulated data by pooling the foci datasets and randomly dividing them into two now groupings of the same size as the Min Volume mm 0 original data sets An ALE image is created for each new data set then subtracted from the other and compared to the true data After many permutations we have a Data Set 1 Output Name L_insula voxel wise P value image showing where the true data s values sit on the distribution of values in that voxel In certain cases a very small or even negative value could Ready Compute be significantly high on the distribution To simplify interpretation of ALE contrast images they are converted to Z scores to show their significance instead of a direct ALE subtraction Cluster analysis of contrast images uses Z score values in the image statistics and maxima 2743 Foci 156 Experiments 107984 mm Settings P Value Permutations 5000 Output Files Data Set 2 Output Name R_insula Figure 4 GingerALE Contrast Interface GingerALE saves the foci data of an ALE analysis in the output image s header Thi
4. MNI space e00 mask_diff nii File Edit View Analysis ROI Image Plugins Window 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 Figure 7 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 some of your resultant ALE clusters may appear to be located outside of the brain when viewed on the Talairach or MNI anatomical templates ALE Method Here you may choose to use the ALE algorithm described by Eickhoff et al 2009 or implement the small 4 correction to minimize within experiment effects described by Turkeltaub et al 2012 In addition since both of these ei 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 N A Figure 7 ss feet Between Mask Size Options PRL PY You may also choose if you want the coordinates of any resultant ALE clusters to be reported for all submaxima in a single
5. ele Ben 11 Sah CONV GLUE E 11 3 8 Help Mem opgeet EENS EEN 12 A CICS GINBOKALE EEN 12 S RE HO MGVICE EE 13 1 About GingerALE GingerALE is used for performing meta analyses of human brain imaging studies with published coordinates in Talairach or MNI space When ALE was originally developed by Peter Turkeltaub it stood for activation likelihood estimation Turkeltaub et al 2002 It has also come to mean anatomic likelihood estimate when used in conjunction with anatomic data such as the voxel based morphometry VBM database BrainMap adopted GingerALE s first methods in 2003 and since then there have been several modifications to keep the algorithms current Thresholding methods described in Laird et al 2005 and Eickhoff et al 2012 have been added With version 2 0 GingerALE switched ALE methods from fixed effects to random effects as well as incorporated variable uncertainty based on subject size Eickhoff et al 2009 A modification to the ALE method described by Turkeltaub et al 2012 limits the effect of a single experiment The full text for these publications is available on brainmap org pubs 2 Performing ALE Meta Analyses The random effects algorithm changed GingerALE s focus from agreement between foci to agreement across experiment groups Or if using Turkeltaub s method of minimizing within group effects GingerALE finds agreement across subject groups Either way your results are driven by your datase
6. template file Colin1 1 nii or the MNI template file Colin27_T1_seg MNI nii from GingerALE s website depending on the space in which your meta analysis was performed b In image window that pops up click on File gt Add Overlay and select the thresholded results image that you created in GingerALE It will be named after the thresholding method and value that you chose E g pNO1 nii _p001 nii FWEOS nii etc This overlays your functional meta analysis results on top of Ui _clust nii 90O Colin27_T1_seg_MNI File Edit View Analysis ROI Image Plugins Window Figure 5 Anatomical underlay in Mango the anatomical template c In the image window choose Edit gt Update Image Range to make sure that all of your results are being shown Very important d 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 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 This is Mango s World Space setting that reads the reference space in the image s header e To change the color map go to the smaller rectangular window and click on the red box on the left side move your curso
7. 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 Output Files Lastly you may specify the output directory for all GingerALE output files and which files you want to be saved Further description of the output files can be found in Section 2 5 Warnings what your preference is for pop up windows about boundary foci and overwriting files 3 2 Open Foci 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 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 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 Shortcut F 3 3 Open ALE Images Contrast analyses use the thresholded ALE images from individual analyses For more on how subtraction analysis works see Section 2 3 Open ALE Image 1 Open ALE Image 2 and Open Pooled ALE Image menu items let you select the files for your fi
8. BrainMap GingerALE 2 3 http www brainmap org Copyright 2003 2013 Research Imaging Institute UTHSCSA User Manual for GingerALE 2 3 Research Imaging Institute UT Health Science Center San Antonio http brainmap org 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 Applications Programmer Angela M Uecker Database Programmer Michaela Robertson Research Scientist Kimberly L Ray Graduate Student Updated 14 June 2013 GingerALE User Manual page 2 Table of Contents A ABOUT Gime erALE eege EE eege 3 2 Performing ALE Meta Analy se sisccssessesessiacesssssecvadsssenscewasnsuceadesseeveessecsous ere ioe eieh Eed 3 ZL FOC ME el 3 2 2 Single Dataset Analy SiS aeiiae onransa a aeaa begat alecg cust dda EAEE Aeee aiee aaeoa de EAn adaa ea laaan aaiae iaa ai deidan 4 23 Comtrast EE 6 24 Connectivity ANAlyS ESen E a a a aE A aa Eea A ASEA a EAE a Ea Ea aara aea aa aa Aaaa iaa a EEEn 7 BCEE BIOS EN A E EE E EA E A E AEAEE E E E E E T deeeeeueoetee 7 2 6 Viewing YOUP RESUltss seenen 8 3 Menu eMis eirinn a a rere rere rrr re rrr rr etre errr renter teers 9 3 1 Rteleteneeg ees ee einir aaa ia aa ascla tbe d asliouedeeacetitbatcanctanereaaeeaarnabvanaranniagteianraeadcunisiantnine 9 ES PZ MOST OCL WEE 10 3 3 Open ALE Here eege EES 10 Si Merge Si Save FOC EE 11 3 5 Save Data HistOry sect dice esn nah atarax tata daca eee ea hanes 11 3 0 EXPOrt
9. E User Manual page 6 2 3 Contrast Analyses To perform a contrast analysis and examine two different sets of foci for statistically significant differences in convergence you must first run 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 GingerALE can help make the pooled data set File gt Save amp Merge Foci Once the pooled analysis is complete you will need the 3 thresholded ALE images that were created in each of those analyses To carry out a subtraction analysis first select the Contrast Studies radio button in the main GingerALE window Open the three thresholded ALE images using OO GingerALE GingerALE the File menu items Open ALE Image 1 Open ALE Image 2 and Open Pooled ALE Image Now that the input Data required data sets are loaded double check your chosen settings for threshold method and value number of permutations and output file names prefix Coordinate System MN then click Compute O Single Study Contrast Studies Data Set 1 L_insula_ALE_pNOO1 Contrast analysis compares and contrasts two ALE R 3 er leet Et periments at oe mn datasets A conjunction image shows the similarity Data Set 2 R_insula_ALE_pNOO1 between the datasets The conjunction is created using 1392 Foci 78
10. airach This will correctly move your coordinates into the Talairach space 3 8 Help Menu About GingerALE This menu item contains basic information about GingerALE such as the homepage version number and GingerALE File Tools Help copyright date On Macintosh computers this menu item is under the GingerALE menu Otherwise it is in the Help menu Figure 9 GingerALE s Main Menus 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 4 Citing GingerALE If you use GingerALE in your research please acknowledge our previous work in any resultant publication For research using a contrast analysis Eickhoff SB Bzdoc D Laird AR Roski C Caspers S Zilles K Fox PT Co activation patters distinguish cortical modules their connectivity and functional differentiation Neuroimage 57 938 949 2011 For research using GingerALE 2 x Eickhoff SB Laird AR Grefkes C Wan
11. are confident that your out of mask foci are correct don t worry foci outside the mask still contribute to the ALE analysis The main window of GingerALE Fig 3 will confirm the name of your foci file the number of foci and foci groups contained therein and the current reference space Once you have loaded your dataset and reviewed any errors or warnings you are now ready to choose your threshold settings and begin the calculations of the analysis The ALE meta analysis calculations follow four main steps ALE scores null distribution thresholding and cluster Statistics ALE calculations first create a 3D image for each foci group using the mask the foci and a Gaussian blur with a FWHM empirically derived from your subject size These pre ALE experiment level images are called Modeled Activation MA maps Eickhoff et al 2009 The MA maps can be calculated by finding the union Eickhoff et al 2009 or the maximum Turkeltaub et al 2012 across each focus s Gaussian Using the maximum limits the effect of an experiment with multiple foci very near one another and is referred to as Non Additive in the preferences Section 3 1 The ALE image is a union of all of the MA maps GingerALE uses the analytical method of determining the null distribution of the ALE statistic Eickhoff et al 2012 This method first tallies the values in the MA maps to make histograms Using histograms changes the computation from voxels to equal va
12. broken into 3 options based on Choose Transform MNI SPM to Talairach what software you used for spatial normalization of your data SPM FSL or Other Output File coords_Tal txt Choose Transform 1 MNI SPM to Talairach 2 MNI FSL to Talairach j Figure 8 Transforming Coordinates between MNI 3 MNI Other to Talairach and Talairach Spaces 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 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 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 Tal
13. d FDR corrected thresholds are not optimal Two new thresholding algorithms Family wise error and Cluster level inference have been added Both simulate random data sets using the same characteristics as your data set number of foci number of foci groups and subject sizes The family wise error method tracks the distribution of maximal ALE scores from each permutation The FWE corrected threshold is set to the ALE value that no more than a specified fraction of the distribution exceeds that value FWE thresholds are more conservative so 5 of random studies or P lt 0 05 is recommended When using cluster level inference the simulated data is thresholded using a cluster forming threshold using FDR or an uncorrected P value GingerALE finds the contiguous volumes above the threshold clusters and tracks the distribution of their volume The cluster level inference corrected threshold sets the cluster minimum volume such that only for example 5 of the simulated data s clusters exceed this size We generally use P lt 0 001 or FDR of 0 01 as a cluster forming threshold and 0 05 for cluster level inference Cluster size thresholds are available when using threshold methods other than cluster level inference you can remove clusters under a user chosen size by using the Min Volume mm setting Fig 3 Whichever threshold algorithm you used GingerALE will compile some statistics on the regions above the threshold The cluster stat
14. e contiguous non zero regions in the thresholded image Each voxel in each region is given an integer value according to which cluster it is in The clusters are sorted by size with 1 assigned to the largest cluster Suffix _clust nii e Cluster Spreadsheet An excel document with 10 columns of information about the result s clusters 1 cluster number with the largest at 1 2 volume of cluster in mm 3 5 x y z values of the weighted center of mass 6 maximum ALE value observed in the cluster 7 9 x y z values of the location of the maximum ALE value 10 Talairach Daemon anatomical label associated with the peak coordinates If your preferences are for a cluster analysis to contain all extrema then columns 6 10 will be repeated in a new row with information on each local maximum Output suffix _clust xls e Data History A text file that contains all the parameters and output file names used in the analysis It also includes any additional information about the different stages of analysis such as the FWHM value range and the total non zero volume in the thresholded image It also includes an expanded cluster analysis with all of the information from the spreadsheet as well as cluster extent and a volumetric Talairach Label analysis File name suffix _clust txt Contrast analysis compares and contrasts two datasets For simplicity these datasets will be referred to as A and B The results of the comparison i
15. f Context Normal Mapping and Activations Activation Only Export your coactivation coordinate results using Export gt Locations GingerALE menu item Open the coordinates in GingerALE and perform a meta analysis as described in Section 2 2 to identify areas of convergence among the coactivation coordinates Further refinements to the method Robinson et al 2012 suggest including additional search criteria such as behavioral domain to add context to the otherwise context less task independent results As Sleuth s database grows so will the generalizability robustness and power of this approach 2 5 Output Files A number of files may be created during a single dataset ALE analysis e ALE Image contains the unthresholded ALE values one computed at every voxel in the brain The file name used to save this file will be your Output Name Prefix setting Fig 3 and the suffix _ALE nii e P Value Image contains each voxel s unthresholded P value File name suffix Pn e Thresholded Image ALE map threshold at a given value This is considered the final output image and is used as the input for contrast analyses It has a variable file name depending on the thresholding method and value chosen For example when using FDR pN lt 0 01 the suffix would be _ALE_pNO1 nii It could also be ALE p001 nii or _ALE_FWE05 nii etc e Cluster Image The first step in cluster analysis is identifying th
16. g 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 and Eickhoff SB Bzdok D Laird AR Kurth F Fox PT Activation likelihood estimation revisited Neuroimage 59 2349 2361 2012 and 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 33 1 13 2012 For research using False Discovery Rate threshold 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 5 References Eickhoff SB Bzdok D Laird AR Kurth F Fox PT Activation likelihood estimation revisited Neuroimage 59 2349 2361 2012 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 33 1 13 2012 Robinson JL Laird AR Glahn DC Blangero J Sanghera MK Pessoa L Fox PM Uecker A Friehs G Young KA Griffin JL Lovallo WR Fox PT The functional connectivity of the human caudate An application of meta analytic connectivity modeling with behavioral filtering Neurolmage 60 117 129 2012
17. his method see Section 2 3 File name suffix Pn Thresholded Images contains Z score images for each voxel above the threshold It s possible with unequally sized datasets to find an area with negative ALE values to have significant convergence To ease interpretation of the thresholded images GingerALE switches from ALE maps to Z score images computed from the P value images The file name suffix depends on the threshold used Cluster Analyses The cluster analysis saves a total of six files a cluster image a cluster spreadsheet and a data history for each of the two directions of the contrast The particulars of each of these files can be found above earlier in this section when describing single datasets The only difference is now the cluster analysis is using Z score images instead of ALE images Suffix 2 6 Viewing Your Results Once the thresholded map has been created you ll need an anatomical underlay in order to view the meta analysis results in context We distribute two templates in Talairach space one general file and one to be used specifically by AFNI and one MNI template Fig 5 on GingerALE s website brainmap org ale Although our nii files are compatible with most medical image viewing software we suggest using Mango to view your meta analysis results rii uthscsa edu mango After installing Mango here are some steps to view your results a Open gt Open Image gt select the Talairach
18. is of meta analysis networks Hum Brain Mapp 25 174 184 2005 Genovese CR Lazar NA Nichols TE Thresholding of statistical maps in functional neuroimaging using the false discovery rate Neuroimage 15 870 878 2002 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
19. istics include volume bounds weighted center and the locations and values at peaks within the region Anatomical labels from the Talairach Daemon talairach org are given to the peaks as well as volumetric label data for the clusters If you are using MNI coordinates are transformed using icbm2tal Lancaster et al 2007 For analyses using FDR a recommended cluster size is included in the statistics This volume is calculated using the false discovery rate and the total volume above the threshold The resulting minimum volume will remove any cluster that was smaller than the allowed false positives leaving clusters that should contain true positives To facilitate network analysis the cluster statistics include a table inspired by Lancaster et al 2005 with the number of activations from each foci group that fall within each cluster The final field in the GingerALE interface Fig 3 sets the file names of your output files The prefix given here will determine the base file name of all output files GingerALE will usually create an unthresholded ALE score image an unthresholded P value image a thresholded ALE image and two statistics text files The preferences Fig 6 allow choosing exactly which files are saved A warning can be shown if any output files would overwrite an existing file All images are saved in NIfTI format http nifti nimh nih gov which can be read by a number of functional neuroimaging software packages GingerAL
20. lues within a single bin This switch also removes spatial information from the process The histograms are divided by the total number of voxels in a MA map to create tables of probabilities of finding each value in a MA map Combining the probabilities yields a table of P values for ALE scores The ALE image and the P value table are used to create a 3D P value image Now that you have a P value image it can be used to set a significance threshold on the ALE scores The simplest threshold is an Uncorrected P value threshold Any voxel where the P value image has a value over the threshold will be set to zero Since the Uncorrected P value method is the least conservative we recommend choosing a very conservative threshold such as P lt 0 001 or 0 0001 Another available method is False Discovery Rate FDR Laird et al 2005 Genovese et al 2002 which controls the rate of false positives to less than the chosen threshold value GingerALE computes the FDR using Tom Nichols algorithm www personal umich edu nichols FDR This algorithm yields two P value thresholds depending on the assumptions you want to make FDR pID is the threshold assuming independence or positive dependence FDR pN makes no assumptions about how the data is correlated FDR pN is more conservative option The RII generally uses the P value threshold returned by FDR pN and a False Discovery Rate of 0 01 As noted in Eickhoff et al 2012 uncorrected P value thresholds an
21. mum 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 For data sets that need to be transformed GingerALE contains all the icbm2tal transforms in Tools gt Convert Foci Please note that we no longer use the Brett transform for conversion of coordinates from MNI space to Talairach space however it is included to allow reconversion of published foci 2 2 Single Dataset Analysis Load your foci data into GingerALE with File gt Open Foci Once you select your foci text file GingerALE will read and verify your dataset with a series of checks As previously mentioned there are checks for mismatching reference spaces missing subject sizes and empty or duplicated foci groups There is also a warning dialog for __ GingerALE Oddball GingerALE Input Data Single Study O Contrast Studies Coordinate System MNI Foci Oddbal 2221 Foci 155 Experiments Settings FDR pN wa 0 05 Min Volume mm 250 Output Files Output Name Prefix Oddball Ready Figure 3 GingerALE Interface Compute any foci in your dataset that are outside of the bounds of the current mask For more on masks see Fig 7 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 If you
22. r 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 our favorites for GingerALE results Integer images such as Cluster images or Foci images should use the Spectrum color map 3 Menu Items 3 1 Preferences The preference window shows the relevant settings for performing ALE calculations and saving output files It is under the GingerALE menu on Macintosh computers and under the File menu otherwise Shortcut Coordinate Space A radio button is available to select which standard space the meta analysis should be performed in Talairach or MNI 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 outside 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 or even lower since implementing the Lancaster transform instead of the Brett transform outside of the mask is sometimes due to author error e g missing negati
23. rdinates 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 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 coordinates that are listed in multiple experiments won t be incorrectly identified as in only one experiment and so these multiple activation coordinates can be found on the resultant output image 3 7 Convert Foci This menu item uses a dialog window as seen in Figure 8 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 0008 Convert Foci Input File coords_MNI txt Choose The first three transforms convert coordinates from MNI C space to Talairach space using the Lancaster transform SA Foci k Experiments icbm2tal This transform is
24. rst second and pooled datasets For more on creating pooled datasets see just below in Section 3 4 These menu items are only enabled when in Contrast Analysis mode Shortcuts 1 2 3 3 4 Merge amp Save Foci This tool will combine the foci from Data Set 1 and Data Set 2 into a pooled data set It automatically merges datasets by removing the second copy of experiments found in both data sets Duplicated experiments should be removed as to not give extra weight to those studies Be careful it s possible for different experiments to have identical foci be incorrectly removed so double check your data It s also possible for a study to be intentionally included into both datasets depending on your contrast analysis So human verification is highly recommended for this step This tool is enabled when both 1 amp 2 datasets are loaded Shortcut M 3 5 Save Data History This menu item allows you to save a text output that summarizes your ALE meta analysis at any point in the procedure If you are in an early stage of the analysis very little will be in the data history possibly only information on the current mask For more information on the Data History file see Section 2 5 Shortcut S 3 6 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 coo
25. s a conjunction image and cluster analysis e Conjunction Image contains the regions that exist in both datasets Specifically this is the voxel wise minimum between two thresholded ALE images So this image is also a thresholded ALE image The output file will be named A_conj_B_ALE nii e Cluster Analysis The cluster analysis saves three files a cluster image a cluster spreadsheet and data history These files contain the same type of results as those described in the single dataset analysis above but apply to your conjunction image They will be named A _conj_B _clust nii A_conj_B_clust xls and A_conj_B_clust txt When contrasting two datasets GingerALE produces results for both directions of the contrast Each of the following steps will produce at least two files one for A gt B and one for B gt A ALE Images contains the unthresholded ALE values one computed at every voxel in the brain GingerALE recreates the unthresholded ALE images of each dataset to create these direct voxel wise subtraction images At this point the A gt B image is the same as 1 times the B gt A image The file names used to save these files will be your Output Name Prefix settings Fig 4 and the suffix _ALE nii P Value Images contains each voxel s unthresholded P value P values are generated through permuting through random re groupings of the modeled activation maps Eickhoff et al 2011 For more information on t
26. s allows the contrast analysis to load the foci data for each dataset out of the image file GingerALE will show a warning if there are identical foci groups in both datasets This warning can be ignored if the same foci group is intentionally in both datasets for example if it has coordinates in both the left insula and right insula Fig 4 GingerALE tries to distinguish between a single foci group present in both data sets and two distinct experiments by checking if the data is duplicated within the pooled data set or not Warnings will be shown if there are foci group from either of the two input datasets that are not in the pooled data or vice versa The contrast analysis is restricted to voxels that were significant in at least one of the three input images 2 4 Connectivity Analyses Meta analytic connectivity modeling MACM can be used to examine the functional connectivity of a specific brain region Robinson et al 2010 MACM is a simple easily adaptable data driven method that is especially useful for identifying connections within an indirect network This method can be performed using Sleuth and GingerALE First acquire an anatomical seed ROI and make sure it conforms to Sleuth s image requirements of square 1mm voxels and a maximum ROI volume of 10 000 mm Next use Sleuth s image search capability to identify patterns of coactivation across the entire database It s recommended to include the Experiment level search criteria o
27. t s foci as well as how they are grouped The foci data is read as a text file which can be generated by hand or from a excel worksheet or exported from a workspace in BrainMap Sleuth It s critical that your input foci data uses the format GingerALE is expecting Fig 1 In order to verify that your foci have been interpreted correctly GingerALE will display the number of foci and the number of foci groups Warnings will also be shown if there are experiments without any foci or if an experiment appears duplicated has exactly the same foci 2 1 Foci Formatting The format for this file should be three columns of numbers x y z coordinates separated with Reference Talairach tabs or spaces Optionally the file can start a line Hui 2000 Acupuncture vs Tactile Stimulation Increases Subjects 13 indicating the standard brain space If included GingerALE will check that the current reference oe Ka 30 59 18 43 space matches the foci space and offer to change 59 ER ou if needed Subsequent foci groups will be 50 18 18 separated by a line break and started with some identifying information Sleuth will export the Li 2003 Conventional Acupuncture gt Rest Activations first author name year and experiment name or Subjects 20 subject group name Next should be the number 5 12 82 33 10 8 of subjects for this group of foci followed by the 2 3 77 71 11 37 coordinate data All non coordinate data should 15 36 62 35
28. ve 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 ONO GingerALE Preferences Coordinate Space Talairach O MNI Mask Size More Conservative Smaller O Less Conservative Larger ALE Method O Eickhoff HBM 2009 Turkeltaub Non Additive HBM 2012 FWHM values are subject based Eickhoff 2009 Additional FWHM mm None Cluster Analysis Peaks All extrema O No Sub Maxima Minima Output Directory Change Desktop Save Output Files for ALE Image M Cluster Image IW P Value Image IW Cluster Spreadsheet IW Thresholded Image Data History Warn me about l Foci Outside Mask T Overwriting Files Figure 6 GingerALE Preferences we recommend that you change the y value from positive to negative before proceeding with ALE Finding coordinates located 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
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