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