This is the description of a Matlab script (classTAL.m) that automatically classifies BrainVoyager .voi maps with afni brain atlas. The script saves many useful output files

Federico D'Agata

English

Crossref

ClassTAL

Federico D&#x27

Nature Precedings

ClassTAL.m Script
We realized a Maltab® script (version 7.0) for voxel of interest (VOI) analysis. Using the AFNI data 
collection  (http://afni.nimh.nih.gov),  we  saved  two  atlas  in  .mat  format,  the  atlas  are  arrays  of 
140x172x120 voxels with a 1x1x1 mm3 resolution. The first has been created for Gyrus classification of 
the normalized brain in the Talairach space (fig. 1) and the second for Brodmann Areas (BA, fig. 2).
Figure 1 Gyrus AFNI Template
Three orthogonal slices of the template showing different Gyrus in different color 
Figure 2 Brodmann Areas AFNI Template
Three orthogonal slices of the template showing different BA in different color 
Next  we  created  other  atlases  forcing  the  classification  of  null  voxels  on  the  basis  of  a  simple 
algorithm:  if  the  absolute  majority  (>50%) of  nearest  voxels  (see  fig.  3  bottom left)  belong to  a 
category we assigned that voxel to it.  Using iteratively the algorithm we saved eight more atlases 
(called R1, R2, R3, R4) with an increasing numbers of classified voxels, but also with some image 
degradation (see fig. 3). 
The inputs of the script were .voi files saved from Brain Voyager QX© (http://www.brainvoyager.com) 
volume maps. This files contained samples of statistically significative voxels, divided in clusters. The 
script can compare them with the selected atlases to produce some outputs described in the following 
paragraphs.
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Figure 3 Brodmann Area AFNI R1 Template
Three orthogonal slices of the template showing different BA in different color after near voxel forced classification
Gyrus Output
In the Gyrus output mode the script produces three graphs using the selected AFNI Gyrus atlas:
• the percentage of active voxels divided by the cerebral gyri (see fig. 4 on the left), the procedure 
stops at a fixed threshold of the total number of voxels (p.e. with a 5% threshold the script 
graphs the gyri that contains a number of active voxel greater than 5% of total active voxel, see 
fig. 4); 
• the lateralization percent of the gyri that overcome the threshold (see fig. 4 on the right);
• the number of active voxels of the supra-threshold areas as a function of the gyrus and of the 
Talairach coordinate X (left to right, see fig. 5).
Figure 4 Gyrus Output 1 & 2
Gyrus counts percent (left) and gyrus lateralization (right)
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Figure 5 Gyrus Output 3
Gyrus counts in function of areas and lateralization
The possible  abbreviations  of  the output  figures  are:  PCC = Posterior  Cingulate;  ACC = Anterior 
Cingulate; SbCG = Subcallosal Gyrus; TTG = Transverse Temporal Gyrus; Unc = Uncus; RG = Rectal 
Gyrus; FG  = Fusiform Gyrus; IOG = Inferior Occipital Gyrus; ITG = Inferior Temporal Gyrus; Ins = 
Insula; PaHG = Parahippocampal Gyrus; LG = Lingual Gyrus; MOG = Middle Occipital Gyrus; OrG 
= Orbital Gyrus; MTG = Middle Temporal Gyrus; STG = Superior Temporal Gyrus; SOG = Superior 
Occipital  Gyrus;  IFG  =  Inferior  Frontal  Gyrus;  Cun  =  Cuneus;  Ang  =  Angular  Gyrus;  SMG  = 
Supramarginal Gyrus; CinG = Cingulate Gyrus; IPL = Inferior Parietal Lobule; Pcun = Precuneus; SPL 
=  Superior  Parietal  Lobule;  MFG = Middle  Frontal  Gyrus;  PaCL =  Paracentral  Lobule;  PoCG = 
Postcentral Gyrus; PrCG = Precentral Gyrus; SFG = Superior Frontal Gyrus; MdFG = Medial Frontal  
Gyrus; vUv = Uvula of Vermis; vPyr = Pyramis of Vermis; vTub = Tuber of Vermis; vDec = Declive of 
Vermis; vCul  = Culmen of Vermis; Cton = Cerebellar Tonsil; SLun = Inferior Semi-Lunar Lobule; Fast 
= Fastigium;  Dent = Dentate; Nod = Nodule; Uvu = Uvula; Pyr = Pyramis; Tub = Tuber; Dec = 
Declive; Cul = Culmen; Clin = Cerebellar Lingual.             
          
Brodmann Areas Output
The Brodmann Areas mode produces the same three graphs described above using a BA AFNI atlas.
The possible abbreviations are: Hippo = Hippocampus; Amg = Amygdala; HyTH = Hypothalamus; SN 
= Substantia Nigra; CauTa = Caudate Tail; CauBo = Caudate Body; CauHd = Caudate Head; VAN = 
Ventral  Anterior  Nucleus;  VPMN =  Ventral  Posterior  Medial  Nucleus;  VPLN = Ventral  Posterior 
Lateral Nucleus; MDN = Medial Dorsal Nucleus; LDN = Lateral Dorsal Nucleus; Pulv = Pulvinar; 
LPN = Lateral  Posterior Nucleus; VLN = Ventral  Lateral  Nucleus; MN = Midline Nucleus; AN = 
Anterior Nucleus; MaBo = Mammillary Body; Md GP = Medial Globus Pallidus; Lt GP = Lateral 
Globus Pallidus; Put = Putamen; NAcc =Nucleus Accumbens; MGB = Medial Geniculum Body; LGB 
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= Lateral Geniculum Body; SuTH = Subthalamic Nucleus; BA 1-47 = Brodmann Area 1-47.
Activation Output
In the Activation mode the voxels are assigned to one of three groups: cerebellar voxels (CRBL), 
subcortical voxels (SCTX) and cortical voxels (CRTX). The relative percents of the groups are graphed 
together  with  their  lateralization  (see  fig.  6,  black  for  left  and white  for  right).  The classification 
proceeds in a serial fashion starting with the AFNI Gyrus atlas (CRTX and CRBL) and finishing the 
remaining voxels with the AFNI BA atlas. The unclassifiable voxels are excluded from the graph (i.e. 
sum of the three groups = 100%). 
Figure 6 Activation Output
Percentages of cortical, subcortical and cerebellar total activation
Lobes Output
In the Lobes mode the cortical voxels are assigned to one of brain's lobes using a AFNI Gyrus atlas.  
The relative percents are graphed together with lateralization (see fig. 7, blue for left and red for right). 
Figure 7 Lobes Output
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Lobes relative activation
Abbreviations: POSTR = Posterior Brain (behind Central Gyrus); ANTER = Anterior Brain (); OCCIP 
= Occipital Lobe; LIMBC = Limbic Lobe; TEMPL = Temporal Lobe; PARTL = Parietal Lobe; FRONT 
= Frontal Lobe.
Subcortical Output
In the Subcortical mode the outpus is a graph of the left (in green) and right (in yellow) fraction of the  
voxels  that are active (i.e 100% = all area's voxels are activated) in some important non cortical areas 
(see fig. 8). The classification uses  a BA AFNI atlas.
Figure 8 Subcortical Output
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Fraction of active non cortical area's voxels
Abbreviations: VERMS = Vermis; CRBLT = Lateral Cerebellum; THALS = Thalamus; GANGL = 
Basal Ganglia; REDNC = Red Nucleus; HYPTH = Hypothalamus; AMYGD = Amygdala; HIPPO = 
Hippocampus.
Segmentation Output
In the Segmentation mode the voxels of the BA or Gyrus mode are saved in .voi or .img (analyze)  
format files (see fig. 9).
Figure 9 Segmentation Output
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In different color voxels from different BA (left) and insular active voxels subsample (right) displayed by Brain Voyager©
Table Output
In Table Mode the outputs is a .txt file with many rows (see tab. 1). Every row represents an area that  
meet some criteria: the number of active voxels included in the area surpasses a fixed fraction of total 
activation voxels (default = 5%) or the number of active voxels surpasses a fixed fraction of the total  
voxels of that area (default = 25%) or the number of active voxels surpasses a fixed absolute number of 
voxels in subcortical areas (default = 125) or the number of active voxels surpasses a minimum fixed 
absolute number of voxels (default = 100).
Every  row contains  the  following data:  name of  the  gyrus  preceded by the  left,  right  or  bilateral 
attribute, number of active voxels, lateralization, Brodmann areas of the voxels group in decrescent 
order.
The maximum number of Brodmann Areas written in the table is fixed (default = 4) to not obscure the 
output readability.
The  output  can  be  of  the  total  activation  voxels  or  cluster  by  cluster  with  also  the  Tailarach's 
coordinates of the peak's activations including their gyrus and Brodmann area specification.
Table 1 Activations Summary
Area Voxels L/R% Left BA Right BA
Bilat Middle Frontal Gyrus 27529 35/65% 9 8 10 46  9 8 10 46  
Bilat Cingulate Gyrus 26379 51/49% 31 24 32 23  31 24 32 23  
Bilat Out of Gyrus 16444 49/51% 23 6 31 9  23 13 6 31  
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Bilat Inferior Parietal Lobule 13035 39/61% 40 13 22 39  40 13 22  
Bilat Superior Frontal Gyrus 8078 48/52% 9 10 6 8  9 10 6 8  
Bilat Supramarginal Gyrus 7561 33/67% 40 39  40 39  
Bilat Inferior Frontal Gyrus 4514 7/93% 46 10  47 46 45 9  
Bilat Insula 3279 1/99% 13 40  13 47 22 21  
Bilat Precuneus 3200 40/60% 7 31 39 19  7 31 5  
Bilat Medial Frontal Gyrus 2642 33/67% 6 9 32 8  6 9 32 8  
Bilat Superior Temporal Gyrus 2539 12/88% 22 13 42 40  22 39 13 42  
Bilat Precentral Gyrus 2503 24/76% 9 6 4 8  9 6 44  
Bilat Paracentral Lobule 1105 52/48% 31 24  31 24  
Bilat Angular Gyrus 833 42/58% 39 40  39 40  
Bilat Posterior Cingulate 724 50/50% 23 23
Bilat Anterior Cingulate 698 65/35% 32 24  32 24  
Right Cuneus 360 0/100% 7 18 19 31  
Right Ventral Lateral Nucleus 319 0/100%
Bilat Postcentral Gyrus 306 87/13% 40 2 42  40 2  
Right Middle Temporal Gyrus 214 0/100% 21 20 39  
Right Medial Dorsal Nucleus 159 0/100%
Right Ventral Posterior Lateral Nucleus 137 0/100%
Table of the total activation 
Download
The script and the atlases (both in .mat or .img format) are available to anyone for examination or use 
at  the  Nature  Preceding site  (http://precedings.nature.com).  For  help  or  support  send an  e-mail  at 
federico.dagata@unito.it. 
Installation
To install  the script  download the .zip file,  extract  all  the files  in  the same directory and add the 
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directory to the paths of matlab (Menu – File – Set Path… – Add Folder…, see fig. 10). 
Figure 10 Installation
Video Capture of the Set Path installation
How to use 
From the Matlab® Command window write “classTAL” and press <CR> key. It will appear a GUI 
window like that of fig. 11. Inside the window there are 4 panels: “Thresholds”, “Output”, “Atlas”, 
“Text file” and two buttons: “Default”, “Go”. 
Inside  “Thresholds”  there are  4 input  boxes  and a  popup menu in which  it  is  possible  to  set  the 
thresholds  of all  the script’s  outputs.  “Cortical”  input  represents  the absolute  minimum number of 
voxels  needed  to  insert  a  cortical  gyrus  in  the  script’s  output.  “Subcortical”  input  represents  the 
absolute minimum number of voxels needed to insert a subcortical area in the script’s output. “Relative 
TOT” input represents the number of voxels (computed as a percent of the total number of voxels, 5% 
in fig. 11) needed to insert an area in the script’s output. “Relative GY” input represents the number of 
voxels inside every gyrus (computed as a percent of the total number of the gyrus, 25% in fig. 11) 
needed to insert that cortical gyrus in the script’s output. The thresholds are applied with a logical OR, 
so to be excluded from the output an area should have less voxels than all the set voxels thresholds.
 “Rows BA” menu represents the number of BA reported in the Table Output for every table rows (see 
tab. 1, with the 4 “Rows BA” setting in the Left and Right BA columns were reported the 4 most 
represented BA). 
Figure 11 Script GUI
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Video Capture of the Graphical User Interface 
Inside “Output” there are 8 check boxes that can be set on or of to select the required outputs (see 
output section above). With the “Filter” check box on the areas under the thresholds are deleted from 
the output saved, but same text is always written in the Matlab® Command Window, the areas that will 
be deleted from the saved file are highlighted with an asterisk “*” (see fig. 20 in the Example below).
Inside “Atlas” there are 2 popup menus with the Atlases (Gyrus R0, R1, R2, R3, R4; Brodmann Area 
R0, R1, R2, R3, R4) used for the classification of the voxels (see above for the description of the  
Atlases).
Inside “Text file” there is the complete file’s path of the fileVOI.txt. This file is a text file that the script  
uses to find the VOIs’ files. FileVOI.txt should be edited with any file editor (e.g. edit command of 
Matlab® or notepad of Windows as in fig.  12),  then the script  searches the listed BrainVoyager© 
VOIs’ files and analyzes them. The VOIs’ files could be as much as one need, they must be one for one  
text row and they must not have the file format specification (i.e.  the final .voi).  If one wants the 
Cluster  table  output  in  the  same  directory  of  the  .voi  file  there  must  be  the  file  with  the  peaks 
coordinates table (a BrainVoyager© .txt file that must have the same name of the .voi file, but with a 
.pk.txt file file format as in fig. 16).
Pressing “Default”  button  the  setting  of  the  GUI are  changed back to  the  defaults  (Cortical=100,  
Subcortical=125, Relative TOT=0.05, Relative GY=0.25, Rows BA=4, no checked into Output saving 
Filter, Gyrus R0 and Brodmann Area R2 for the Atlas).
Pressing “Go” button the script will be executed, the output will be shown in the Matlab® Command 
window and saved in the same directory of the VOIs files. The output will be multiple on the basis of 
the color of voxels in the .voi file: orange (i.e. RGB 255, 75, 0 in the Select Color window of the menu 
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Analysis – Region-of-Interest Analysis – Edit; see fig. 17) would be activation voxels, blue (i.e. RGB 
0, 75, 255; see fig. 17) deactivation voxels and everything else would be not specified or other. All the 
output will have a “_Activ”, “_Deact” or “_Other” suffix on the basis of the color. 
The Gyrus output produces 3 .bmp files named as the original VOI file (multiplied for _Activ, _Deact 
and _Other subsamples) with a “GY”, “GY3D” and “GYlat” at the end (output 1, 2 and 3, fig. 4, 5).
The Brodmann output produces 3 .bmp files (multiplied for _Activ, _Deact and _Other subsamples) 
with a “BA”, “BA3D” and “BAlat” at the end (same as output 1, 2 and 3, fig. 4, 5, but with the BA 
atlas instead of the Gyrus Atlas; fig. 4 and 5). 
The Division output produce 3 .bmp files (multiplied for _Activ, _Deact and _Other subsamples) with a 
“PART”, “LOBE” and “SUB” at the end (fig. 6, 7, 8).
The Tab Cluster and Tab Total outputs produce 1 .txt file (multiplied for _Activ, _Deact and _Other 
subsamples) each (with a  final “_Clust” for the first) with a table like tab. 1 (with the peaks voxels  
classification and in separated clusters for Tab Cluster).
The Analyze and Brain Voyager outputs produce 2 kind of files each (1 for Gyrus and 1 for BA) with 
the Segmentation output maps (see fig. 9). The 4 Analyze files (.hdr plus .img) will be named “_GYtot” 
and “BAtot”, the 2 Brain Voyager files (.voi) will be named “_bvq_gy” and “_bvq_ba”. 
Figure 12 Editing VOIs paths
Video Capture of the fileVOI.txt content 
Example 
Here is a step by step example on the way to use the script.
1. Open a .vmp of interest in BrainVoyager© with a map of an experimental contrast.
2. Use the Option – Create Volume-Of-Interest From Map Cluster command (fig. 13) to create clusters 
VOI (fig. 14).
Figure 13 From .vmp to .voi
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Video Capture of the conversion of a statistical parametric map into a VOI file 
Figure 14 Saving the VOI file
Video Capture of the VOI saving 
3. Save the file .voi in a directory (fig. 14). Use the notepad (fig. 12) to modify the fileVOI.txt to point  
to the .voi file.
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4. If you want also the Tab Cluster output you must save the .pk.txt file in the same directory of the .voi 
file. To do so use the Option – VOI Functions – Table button in the Analysis – Volume-Of-Interest 
panel (fig. 15, 16).
Figure 15 Opening Peaks Table
Video Capture of the opening of the Peaks Table .pk.txt file
5.  If  necessary  edit  the  clusters  (Select  Color  window of  the  menu Analysis  –  Region-of-Interest 
Analysis – Edit; see fig. 17) to be sure that activated voxels are in orange color (RGB 255, 75, 0) and 
deactivated voxels are in blue color (RGB 0, 75, 255).
6. Set the thresholds, the atlas and the output you want (fig. 11)
7. Press the Go button to execute the script.
8. You can look at the output in the Command window and if you want you can copy and paste the 
texual output.
9. The script saves the selected outputs in files inside the directory of VOIs files.
10. You can run again the script with other settings overwriting the files.
Figure 16 Saving Peak Table
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Video Capture of the of the creation of the Peaks Table .pk.txt file
Figure 17 Color Editing
Video Capture of the Select Color panel 
Figure 18 Command Window Output
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Video Capture of the Matlab® textual output 
Figure 19 Script Running
Video Capture of the script running and saving output files 
Figure 20 Output Files 
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Video Capture of the directory with the saved outputs 
Compatibility
The script was tested with Matlab® 7.x.x and Brain Voyager QX© 1.x.x 2.x.x without any problems. 
We do not guarantee for its functioning with other versions and we are not responsible for any possible 
malfunctioning or subsequent inconvenient.
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D'Agata, Federico

Institutional Research Information System University of Turin

classTAL

This is the description of a Matlab script (classTAL.m) that automatically classifies BrainVoyager .voi maps with afni, MRIStudio white matter and fcon1000 Intrinsic Connectivity Networks brain atlas. The script saves many useful output files (tables, figures and .voi)

ClassTAL.m Script
We realized a Maltab® script (version 7.0) for voxel of interest (VOI) analysis. Using the AFNI data 
collection  (http://afni.nimh.nih.gov),  we  saved  two  atlas  in  .mat  format,  the  atlas  are  arrays  of 
140x172x120 voxels with a 1x1x1 mm3 resolution. The first has been created for Gyrus classification of 
the normalized brain in the Talairach space (fig. 1) and the second for Brodmann Areas (BA, fig. 2).
Figure 1 Gyrus AFNI Template
Three orthogonal slices of the template showing different Gyrus in different color 
Figure 2 Brodmann Areas AFNI Template
Three orthogonal slices of the template showing different BA in different color 
Next  we  created  other  atlases  forcing  the  classification  of  null  voxels  on  the  basis  of  a  simple 
algorithm:  if  the  absolute  majority  (>50%) of  nearest  voxels  (see  fig.  3  bottom left)  belong to  a 
category we assigned that voxel to it.  Using iteratively the algorithm we saved eight more atlases 
(called R1, R2, R3, R4) with an increasing numbers of classified voxels, but also with some image 
degradation (see fig. 3). 
The inputs of the script were .voi files saved from Brain Voyager QX© (http://www.brainvoyager.com) 
volume maps. This files contained samples of statistically significative voxels, divided in clusters. The 
script can compare them with the selected atlases to produce some outputs described in the following 
paragraphs.
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Figure 3 Brodmann Area AFNI R1 Template
Three orthogonal slices of the template showing different BA in different color after near voxel forced classification
Gyrus Output
In the Gyrus output mode the script produces three graphs using the selected AFNI Gyrus atlas:
• the percentage of active voxels divided by the cerebral gyri (see fig. 4 on the left), the procedure 
stops at a fixed threshold of the total number of voxels (p.e. with a 5% threshold the script 
graphs the gyri that contains a number of active voxel greater than 5% of total active voxel, see 
fig. 4); 
• the lateralization percent of the gyri that overcome the threshold (see fig. 4 on the right);
• the number of active voxels of the supra-threshold areas as a function of the gyrus and of the 
Talairach coordinate X (left to right, see fig. 5).
Figure 4 Gyrus Output 1 & 2
Gyrus counts percent (left) and gyrus lateralization (right)
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Figure 5 Gyrus Output 3
Gyrus counts in function of areas and lateralization
The possible  abbreviations  of  the output  figures  are:  PCC = Posterior  Cingulate;  ACC = Anterior 
Cingulate; SbCG = Subcallosal Gyrus; TTG = Transverse Temporal Gyrus; Unc = Uncus; RG = Rectal 
Gyrus; FG  = Fusiform Gyrus; IOG = Inferior Occipital Gyrus; ITG = Inferior Temporal Gyrus; Ins = 
Insula; PaHG = Parahippocampal Gyrus; LG = Lingual Gyrus; MOG = Middle Occipital Gyrus; OrG 
= Orbital Gyrus; MTG = Middle Temporal Gyrus; STG = Superior Temporal Gyrus; SOG = Superior 
Occipital  Gyrus;  IFG  =  Inferior  Frontal  Gyrus;  Cun  =  Cuneus;  Ang  =  Angular  Gyrus;  SMG  = 
Supramarginal Gyrus; CinG = Cingulate Gyrus; IPL = Inferior Parietal Lobule; Pcun = Precuneus; SPL 
=  Superior  Parietal  Lobule;  MFG = Middle  Frontal  Gyrus;  PaCL =  Paracentral  Lobule;  PoCG = 
Postcentral Gyrus; PrCG = Precentral Gyrus; SFG = Superior Frontal Gyrus; MdFG = Medial Frontal  
Gyrus; vUv = Uvula of Vermis; vPyr = Pyramis of Vermis; vTub = Tuber of Vermis; vDec = Declive of 
Vermis; vCul  = Culmen of Vermis; Cton = Cerebellar Tonsil; SLun = Inferior Semi-Lunar Lobule; Fast 
= Fastigium;  Dent = Dentate; Nod = Nodule; Uvu = Uvula; Pyr = Pyramis; Tub = Tuber; Dec = 
Declive; Cul = Culmen; Clin = Cerebellar Lingual.             
          
Brodmann Areas Output
The Brodmann Areas mode produces the same three graphs described above using a BA AFNI atlas.
The possible abbreviations are: Hippo = Hippocampus; Amg = Amygdala; HyTH = Hypothalamus; SN 
= Substantia Nigra; CauTa = Caudate Tail; CauBo = Caudate Body; CauHd = Caudate Head; VAN = 
Ventral  Anterior  Nucleus;  VPMN =  Ventral  Posterior  Medial  Nucleus;  VPLN = Ventral  Posterior 
Lateral Nucleus; MDN = Medial Dorsal Nucleus; LDN = Lateral Dorsal Nucleus; Pulv = Pulvinar; 
LPN = Lateral  Posterior Nucleus; VLN = Ventral  Lateral  Nucleus; MN = Midline Nucleus; AN = 
Anterior Nucleus; MaBo = Mammillary Body; Md GP = Medial Globus Pallidus; Lt GP = Lateral 
Globus Pallidus; Put = Putamen; NAcc =Nucleus Accumbens; MGB = Medial Geniculum Body; LGB 
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= Lateral Geniculum Body; SuTH = Subthalamic Nucleus; BA 1-47 = Brodmann Area 1-47.
Activation Output
In the Activation mode the voxels are assigned to one of three groups: cerebellar voxels (CRBL), 
subcortical voxels (SCTX) and cortical voxels (CRTX). The relative percents of the groups are graphed 
together  with  their  lateralization  (see  fig.  6,  black  for  left  and white  for  right).  The classification 
proceeds in a serial fashion starting with the AFNI Gyrus atlas (CRTX and CRBL) and finishing the 
remaining voxels with the AFNI BA atlas. The unclassifiable voxels are excluded from the graph (i.e. 
sum of the three groups = 100%). 
Figure 6 Activation Output
Percentages of cortical, subcortical and cerebellar total activation
Lobes Output
In the Lobes mode the cortical voxels are assigned to one of brain's lobes using a AFNI Gyrus atlas.  
The relative percents are graphed together with lateralization (see fig. 7, blue for left and red for right). 
Figure 7 Lobes Output
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Lobes relative activation
Abbreviations: POSTR = Posterior Brain (behind Central Gyrus); ANTER = Anterior Brain (); OCCIP 
= Occipital Lobe; LIMBC = Limbic Lobe; TEMPL = Temporal Lobe; PARTL = Parietal Lobe; FRONT 
= Frontal Lobe.
Subcortical Output
In the Subcortical mode the outpus is a graph of the left (in green) and right (in yellow) fraction of the  
voxels  that are active (i.e 100% = all area's voxels are activated) in some important non cortical areas 
(see fig. 8). The classification uses  a BA AFNI atlas.
Figure 8 Subcortical Output
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Fraction of active non cortical area's voxels
Abbreviations: VERMS = Vermis; CRBLT = Lateral Cerebellum; THALS = Thalamus; GANGL = 
Basal Ganglia; REDNC = Red Nucleus; HYPTH = Hypothalamus; AMYGD = Amygdala; HIPPO = 
Hippocampus.
Segmentation Output
In the Segmentation mode the voxels of the BA or Gyrus mode are saved in .voi or .img (analyze)  
format files (see fig. 9).
Figure 9 Segmentation Output
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In different color voxels from different BA (left) and insular active voxels subsample (right) displayed by Brain Voyager©
Table Output
In Table Mode the outputs is a .txt file with many rows (see tab. 1). Every row represents an area that  
meet some criteria: the number of active voxels included in the area surpasses a fixed fraction of total 
activation voxels (default = 5%) or the number of active voxels surpasses a fixed fraction of the total  
voxels of that area (default = 25%) or the number of active voxels surpasses a fixed absolute number of 
voxels in subcortical areas (default = 125) or the number of active voxels surpasses a minimum fixed 
absolute number of voxels (default = 100).
Every  row contains  the  following data:  name of  the  gyrus  preceded by the  left,  right  or  bilateral 
attribute, number of active voxels, lateralization, Brodmann areas of the voxels group in decrescent 
order.
The maximum number of Brodmann Areas written in the table is fixed (default = 4) to not obscure the 
output readability.
The  output  can  be  of  the  total  activation  voxels  or  cluster  by  cluster  with  also  the  Tailarach's 
coordinates of the peak's activations including their gyrus and Brodmann area specification.
Table 1 Activations Summary
Area Voxels L/R% Left BA Right BA
Bilat Middle Frontal Gyrus 27529 35/65% 9 8 10 46  9 8 10 46  
Bilat Cingulate Gyrus 26379 51/49% 31 24 32 23  31 24 32 23  
Bilat Out of Gyrus 16444 49/51% 23 6 31 9  23 13 6 31  
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Bilat Inferior Parietal Lobule 13035 39/61% 40 13 22 39  40 13 22  
Bilat Superior Frontal Gyrus 8078 48/52% 9 10 6 8  9 10 6 8  
Bilat Supramarginal Gyrus 7561 33/67% 40 39  40 39  
Bilat Inferior Frontal Gyrus 4514 7/93% 46 10  47 46 45 9  
Bilat Insula 3279 1/99% 13 40  13 47 22 21  
Bilat Precuneus 3200 40/60% 7 31 39 19  7 31 5  
Bilat Medial Frontal Gyrus 2642 33/67% 6 9 32 8  6 9 32 8  
Bilat Superior Temporal Gyrus 2539 12/88% 22 13 42 40  22 39 13 42  
Bilat Precentral Gyrus 2503 24/76% 9 6 4 8  9 6 44  
Bilat Paracentral Lobule 1105 52/48% 31 24  31 24  
Bilat Angular Gyrus 833 42/58% 39 40  39 40  
Bilat Posterior Cingulate 724 50/50% 23 23
Bilat Anterior Cingulate 698 65/35% 32 24  32 24  
Right Cuneus 360 0/100% 7 18 19 31  
Right Ventral Lateral Nucleus 319 0/100%
Bilat Postcentral Gyrus 306 87/13% 40 2 42  40 2  
Right Middle Temporal Gyrus 214 0/100% 21 20 39  
Right Medial Dorsal Nucleus 159 0/100%
Right Ventral Posterior Lateral Nucleus 137 0/100%
Table of the total activation 
Download
The script and the atlases (both in .mat or .img format) are available to anyone for examination or use 
at  the  Nature  Preceding site  (http://precedings.nature.com).  For  help  or  support  send an  e-mail  at 
federico.dagata@unito.it. 
Installation
To install  the script  download the .zip file,  extract  all  the files  in  the same directory and add the 
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directory to the paths of matlab (Menu – File – Set Path… – Add Folder…, see fig. 10). 
Figure 10 Installation
Video Capture of the Set Path installation
How to use 
From the Matlab® Command window write “classTAL” and press <CR> key. It will appear a GUI 
window like that of fig. 11. Inside the window there are 4 panels: “Thresholds”, “Output”, “Atlas”, 
“Text file” and two buttons: “Default”, “Go”. 
Inside  “Thresholds”  there are  4 input  boxes  and a  popup menu in which  it  is  possible  to  set  the 
thresholds  of all  the script’s  outputs.  “Cortical”  input  represents  the absolute  minimum number of 
voxels  needed  to  insert  a  cortical  gyrus  in  the  script’s  output.  “Subcortical”  input  represents  the 
absolute minimum number of voxels needed to insert a subcortical area in the script’s output. “Relative 
TOT” input represents the number of voxels (computed as a percent of the total number of voxels, 5% 
in fig. 11) needed to insert an area in the script’s output. “Relative GY” input represents the number of 
voxels inside every gyrus (computed as a percent of the total number of the gyrus, 25% in fig. 11) 
needed to insert that cortical gyrus in the script’s output. The thresholds are applied with a logical OR, 
so to be excluded from the output an area should have less voxels than all the set voxels thresholds.
 “Rows BA” menu represents the number of BA reported in the Table Output for every table rows (see 
tab. 1, with the 4 “Rows BA” setting in the Left and Right BA columns were reported the 4 most 
represented BA). 
Figure 11 Script GUI
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Video Capture of the Graphical User Interface 
Inside “Output” there are 8 check boxes that can be set on or of to select the required outputs (see 
output section above). With the “Filter” check box on the areas under the thresholds are deleted from 
the output saved, but same text is always written in the Matlab® Command Window, the areas that will 
be deleted from the saved file are highlighted with an asterisk “*” (see fig. 20 in the Example below).
Inside “Atlas” there are 2 popup menus with the Atlases (Gyrus R0, R1, R2, R3, R4; Brodmann Area 
R0, R1, R2, R3, R4) used for the classification of the voxels (see above for the description of the  
Atlases).
Inside “Text file” there is the complete file’s path of the fileVOI.txt. This file is a text file that the script  
uses to find the VOIs’ files. FileVOI.txt should be edited with any file editor (e.g. edit command of 
Matlab® or notepad of Windows as in fig.  12),  then the script  searches the listed BrainVoyager© 
VOIs’ files and analyzes them. The VOIs’ files could be as much as one need, they must be one for one  
text row and they must not have the file format specification (i.e.  the final .voi).  If one wants the 
Cluster  table  output  in  the  same  directory  of  the  .voi  file  there  must  be  the  file  with  the  peaks 
coordinates table (a BrainVoyager© .txt file that must have the same name of the .voi file, but with a 
.pk.txt file file format as in fig. 16).
Pressing “Default”  button  the  setting  of  the  GUI are  changed back to  the  defaults  (Cortical=100,  
Subcortical=125, Relative TOT=0.05, Relative GY=0.25, Rows BA=4, no checked into Output saving 
Filter, Gyrus R0 and Brodmann Area R2 for the Atlas).
Pressing “Go” button the script will be executed, the output will be shown in the Matlab® Command 
window and saved in the same directory of the VOIs files. The output will be multiple on the basis of 
the color of voxels in the .voi file: orange (i.e. RGB 255, 75, 0 in the Select Color window of the menu 
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Analysis – Region-of-Interest Analysis – Edit; see fig. 17) would be activation voxels, blue (i.e. RGB 
0, 75, 255; see fig. 17) deactivation voxels and everything else would be not specified or other. All the 
output will have a “_Activ”, “_Deact” or “_Other” suffix on the basis of the color. 
The Gyrus output produces 3 .bmp files named as the original VOI file (multiplied for _Activ, _Deact 
and _Other subsamples) with a “GY”, “GY3D” and “GYlat” at the end (output 1, 2 and 3, fig. 4, 5).
The Brodmann output produces 3 .bmp files (multiplied for _Activ, _Deact and _Other subsamples) 
with a “BA”, “BA3D” and “BAlat” at the end (same as output 1, 2 and 3, fig. 4, 5, but with the BA 
atlas instead of the Gyrus Atlas; fig. 4 and 5). 
The Division output produce 3 .bmp files (multiplied for _Activ, _Deact and _Other subsamples) with a 
“PART”, “LOBE” and “SUB” at the end (fig. 6, 7, 8).
The Tab Cluster and Tab Total outputs produce 1 .txt file (multiplied for _Activ, _Deact and _Other 
subsamples) each (with a  final “_Clust” for the first) with a table like tab. 1 (with the peaks voxels  
classification and in separated clusters for Tab Cluster).
The Analyze and Brain Voyager outputs produce 2 kind of files each (1 for Gyrus and 1 for BA) with 
the Segmentation output maps (see fig. 9). The 4 Analyze files (.hdr plus .img) will be named “_GYtot” 
and “BAtot”, the 2 Brain Voyager files (.voi) will be named “_bvq_gy” and “_bvq_ba”. 
Figure 12 Editing VOIs paths
Video Capture of the fileVOI.txt content 
Example 
Here is a step by step example on the way to use the script.
1. Open a .vmp of interest in BrainVoyager© with a map of an experimental contrast.
2. Use the Option – Create Volume-Of-Interest From Map Cluster command (fig. 13) to create clusters 
VOI (fig. 14).
Figure 13 From .vmp to .voi
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Video Capture of the conversion of a statistical parametric map into a VOI file 
Figure 14 Saving the VOI file
Video Capture of the VOI saving 
3. Save the file .voi in a directory (fig. 14). Use the notepad (fig. 12) to modify the fileVOI.txt to point  
to the .voi file.
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4. If you want also the Tab Cluster output you must save the .pk.txt file in the same directory of the .voi 
file. To do so use the Option – VOI Functions – Table button in the Analysis – Volume-Of-Interest 
panel (fig. 15, 16).
Figure 15 Opening Peaks Table
Video Capture of the opening of the Peaks Table .pk.txt file
5.  If  necessary  edit  the  clusters  (Select  Color  window of  the  menu Analysis  –  Region-of-Interest 
Analysis – Edit; see fig. 17) to be sure that activated voxels are in orange color (RGB 255, 75, 0) and 
deactivated voxels are in blue color (RGB 0, 75, 255).
6. Set the thresholds, the atlas and the output you want (fig. 11)
7. Press the Go button to execute the script.
8. You can look at the output in the Command window and if you want you can copy and paste the 
texual output.
9. The script saves the selected outputs in files inside the directory of VOIs files.
10. You can run again the script with other settings overwriting the files.
Figure 16 Saving Peak Table
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Video Capture of the of the creation of the Peaks Table .pk.txt file
Figure 17 Color Editing
Video Capture of the Select Color panel 
Figure 18 Command Window Output
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Video Capture of the Matlab® textual output 
Figure 19 Script Running
Video Capture of the script running and saving output files 
Figure 20 Output Files 
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Video Capture of the directory with the saved outputs 
Compatibility
The script was tested with Matlab® 7.x.x and Brain Voyager QX© 1.x.x 2.x.x without any problems. 
We do not guarantee for its functioning with other versions and we are not responsible for any possible 
malfunctioning or subsequent inconvenient.
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http://precedings.nature.com/documents/6142/version/2

ClassTAL

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