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Doxygen Source Code Documentation
GroupAna.m File Reference
Go to the source code of this file.
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Functions |
| | diary ('diary') |
save all subsequent command
window input and most of the
resulting command window output
to be appended to file diary | fprintf ('\nPlease read the following carefully about group analysis setup:\n') |
| | fprintf ('\n\t1.If the resolution of your EPI data is near n millimeters, during Talairach conversion use\n') |
| | fprintf ('\t"the command adwarp -dxyz n"to greatly reduce runtime without sacrificing accuracy.\n') |
| | fprintf ('\n\t2.We strongly suggest that factor names be labeled with short(2 or 3 capital letters) names\n') |
| | fprintf ('\t so that subbrik labels can be shown on AFNI viewer.\n') |
| | fprintf ('\n\t3.With nesting, arrange your design in such a way that the last factor is nested within the 1st factor.\n') |
| | fprintf ('\n\t4.The program can only handle balanced design now.\n') |
| | fprintf ('\n\t4.Each input file should include only one subbrik.We suggest files be\n') |
| | fprintf ('\t named by reflecting the hierarchy of the experiment design.\n') |
| | fprintf ('\n\t5.Currently all of the following terms are modeled:main effects and applicable interactions in various orders,.\n') |
| | fprintf ('\n\t6.One covariate is currently allowed in the analysis, which should be in the format of one-column text file.\n') |
| | fprintf ('\t The column length has to be the same as the total number of input files.\n') |
| | if (data_type~=0 &data_type~=1) |
| | fprintf (2,'Error:wrong input!Please try it again.\n') |
| | if (data_type==1) = BrikInfo(file(1).nm) |
| | fprintf (1, '\nProgram @Purify_1D can be used to extract the regressor coefficient column to a 1D file.') |
| | if (isnumeric(node_n)==0|isempty(node_n)) |
| | fprintf (2,'Error:the input is not a number.Please try it again.\n') |
| | if (isnumeric(NF)==0|isempty(NF)) |
| end end switch NF | fprintf ('\nAvailable design types:\n') |
| | fprintf ('\n\tType 1:one factor with fixed effect.\n') |
| | fprintf ('\nAvailabe design types:\n') |
| | fprintf ('\n\tType 1:Factorial(crossed) design AXB-both factors are fixed.\n') |
| | fprintf ('\n\tType 2:Factorial(crossed) design AXB-factor A is fixed while B is random.If B is subject, it is') |
| | fprintf ('\n\t usually called 1-way design with A varying within subject.Notice:It is inappropriate to') |
| | fprintf ('\n\t run any constrasts including mean estimates and differences for factor B with this design type.\n') |
| | fprintf ('\n\tType 3:Factorial(crossed) design AXB-both factors are random.\n') |
| | fprintf ('\n\tType 1:Factorial(crossed) design AXBXC-all factors are fixed.\n') |
| | fprintf ('\n\tType 2:Factorial(crossed) design AXBXC-factors A and B are fixed while C is random.If C is subject, it is') |
| | fprintf ('\n\t usually called 2-way design with A and B varying within subject.Notice:It is inappropriate to') |
| | fprintf ('\n\t run any constrast tests including mean estimates and differences for factor C with this design type.\n') |
| | fprintf ('\n\tType 3:Mixed design BXC(A)-A and B are fixed while C(usually subject) is random and nested within A.\n') |
| | fprintf ('\n\tType 4:Mixed design BXC(A)-Fixed factor C is nested within fixed factor A while B(usually subject) is random.\n') |
| | fprintf ('\n\tType 1:Factorial(crossed) design AXBXCXD-all 4 factors are fixed.\n') |
| | fprintf ('\n\tType 2:Factorial(crossed) design AXBXCXD-only factor D is random.If D is subject it is also') |
| | fprintf ('\n\t called 3-way design with all 3 factors A, B, and C varying within subject.') |
| | fprintf ('\n\tType 3:Mixed design BXCXD(A)-only the nested(4th) factor D(usually subject) is random.') |
| | fprintf ('\n\t Also called 3-way design with factors B and C varying within subject and factor A between subjects.') |
| | fprintf ('\n\tType 4:Mixed design BXCXD(A)-D is nested within A, but only the 3rd factor(usually subject)') |
| | fprintf ('\n\t is random.') |
| | fprintf ('\n\tType 5:Mixed design CXD(AXB)-only the nested(4th) factor D(usually subject) is random,') |
| | fprintf ('\n\t but factor D is nested within both factors A and B.If D is subject it is also called 3-way') |
| | fprintf ('\n\t design with factor D varying within-subject and factors A and B between-subjects.\n') |
| | fprintf ('\nNotice:This is NOT an exhaustive list of design types for 4-way ANOVA.Other types might be implemented upon request.\n') |
| | fprintf ('\n\tType 1:Factorial(crossed) design AXBXCXDXE-all 5 factors are fixed.\n') |
| | fprintf ('\n\tType 2:Factorial(crossed) design AXBXCXDXE-only factor E is random.If E is subject it is also') |
| | fprintf ('\n\t called 4-way design with all 4 factors A, B, C and D varying within subject.\n') |
| | fprintf ('\n\tType 3:Mixed design BXCXDXE(A)-only the nested(5th) factor E(usually subject) is random.') |
| | fprintf ('\n\t Also called 4-way design with factors B, C and D varying within subject and factor A between subjects.\n') |
| | fprintf ('\n\tType 4:Mixed design BXCXDXE(A)-the 5th factor E is nested within factor A, but factor D(usually subject)') |
| | fprintf ('\n\t is random.\n') |
| | if (isnumeric(dsgn)==0|isempty(dsgn)) |
| | fprintf (2,'Error:input is not a number.Please try it again.\n') |
| | if (isnumeric(slices)==0|isempty(slices)) |
| | if (unbalanced.yes~=0 &unbalanced.yes~=1) |
| | fprintf (2,'Error:inapproriate input.Please try it again.\n') |
| end | if (unbalanced.yes==1) |
| end | fprintf ('\nThe following two kinds of unbalanced designs are currently allowed:\n') fprintf('\n(1) All factors are fixed- ') |
| | fprintf ('\n\t 1-way ANOVA;2-way ANOVA type 1:AXB;and 3-way ANOVA type 1:AXBXC') |
| | fprintf ('\n\n(2) When a random factor(subject) is nested within another factor A,') |
| | fprintf ('\n\t each level of factor A contains a unique and unequal number of subjects- ') |
| | fprintf ('\n\t 3-way ANOVA type 3:BXC(A);and 4-way ANOVA type 3:BXCXD(A)') if(input('\n\nDoes your unbalanced design belong to either of the above types?(1-Yes |
| id | No () |
| | while (1) |
| | fprintf (2,'Halted:Ctrl+c to exit') |
| end end end | fprintf ('\nTwo kinds of unbalanced design are considered:\n') |
| | fprintf ('\nType 1:When subject is a random factor and nested within another factor(3-way ANOVA type 3, 4-way ANOVA types 3 and 5),') |
| | fprintf ('\n\t there can be different number of subjects for each level of factor A;\n') |
| | fprintf ('\nType 2:Not type 1, but there are different sample sizes for some cells(factor level combinations).') |
| | fprintf ('\n\t For example, add somethint here later...\n') |
| | if (unbalanced.type~=1 &unbalanced.type~=2) |
| end end | for (ii=1:1:5) FL(ii).N_level=0 |
| id | flg () |
| | if ((NF==1|NF==2|NF==3|NF==4)&dsgn==1) |
| id | ANCOVA: ('\nLabel for No.%i ', i fprintf) |
| | FL (i).expr = input('have? ') |
| Factor Label i | fprintf (2,'How many levels does factor%c(%s) ', 64+i, FL(i).expr) |
| | if (isnumeric(FL(i).N_level)==0|isempty(FL(i).N_level)) |
| | fprintf (2,'Error:the input is not a number.Please try again.\n') |
| end | for (j=1:1:FL(i).N_level) |
| end | fprintf ('Label for No.%i level of factor%c(%s)', j, 64+i, FL(i).expr) |
| end | sz (i) |
total number of combinations
end end | if (((NF==3|NF==4)&dsgn==3)) |
total number of combinations
end end | fprintf ('\nLabel for No.%i ', i) |
| | fprintf (2, '\nLabel for No.%i ', NF) |
| | FL (NF).expr = input('have? ') |
| Label this unbalanced factor | fprintf (2, '\nNote:Since this is a nested design the label for levels(usuall subject names) of factor No.%i(%c-%s)', NF, 64+NF, FL(NF).expr) |
| | fprintf (2, '\nhas to be DIFFERENT for each level of factor%c(%s)!!!\n\n', 64+1, FL(1).expr) |
| | fprintf (2,'How many levels does factor%c(%s) corresponding to level%i(%s) of factor%c(%s) ',...64+NF, FL(NF).expr, i, FL(1).level(i).expr, 64+1, FL(1).expr) |
unbalanced levels for this
factor | fprintf ('Label for No.%i level of factor%c(%s) in group%i of factor%c(%s)', j, 64+NF, FL(NF).expr, i, 64+1, FL(1).expr) |
This is for positioning those
contrast columns in the design
matrix in PreProc m end | if (length(unique(combine))==max([FL(NF).UL(:).N_level])) |
| | elseif (length(unique(combine))==sum([FL(NF).UL(:).N_level])) |
| | fprintf (2, '\nError:There is some overlap among the labels of factor%c(%s) across the groups of factor%c(%s)!\n',...64+NF, FL(NF).expr, 64+1, FL(1).expr) |
total number of combinations
end end | if (unbalanced) if~((NF |
| | FL (NF+1).N_level = 1 |
total number of factor combinations
including repeats | sz (NF+1) |
| | if (cov.do~=0 &cov.do~=1) |
end end Only allow one covariate
now | if (cov.do) |
This is for PreProc m to get
the correct shift position | if (NF==2 &dsgn==3) |
'\nThe 2-way ANCOVA for this
design is currently NOT available.\n' | fprintf () |
| | fprintf ('The 1D file for the covariate has to be in the format of one-column text.\n') |
| | fprintf ('And the column should have exactly the same number and order of those input files.\n') |
| | if (fid0==-1) |
| | fprintf (2,'Error:File%s does not exist.Please try it again.\n', cov.FN) |
| | if (count~=ntot &~((NF==1|NF==2|NF==3)&dsgn==1)) |
| Check length of the D file | fprintf (2, '\nError:The column length of the covariate has to equal to the total number of input files!\n') |
| while | fprintf ('\nIs input in the format of one-subbrik-one-file or one-file-per-subject?\n') |
| | if (file_format~=0 &file_format~=1) |
| end end | fprintf ('\nAll input files are supposed to contain only one subbrik.\n') |
| | if (isnumeric(file_num)==0|isempty(file_num)|isnumeric(file_SB)==0|isempty(file_SB)) |
| end | if (file_num *file_SB~=ntot) |
| end | fprintf (2, '\nError:The number of files and subbriks are not consistent!\n') |
| end end | if (file_format==0) if(file_format |
| | if (corr==0) |
| | fprintf (2,'Error:Check the inconsistency.\n') |
| dsgn==1 | FI () |
| | if (isnumeric(ntot)==0|isempty(ntot)) |
| end switch NF | fprintf (2,'\nFor factor%c(%s) at level%i(%s),', 64+1, FL(1).expr, ii, FL(1).level(ii).expr) |
| | fprintf (2,'\nProvide those%i input files:\n', sz) |
| | for (rr=1:1:sz) |
| | GP (1, FI) |
| while | fprintf (2,'No.%i file ', rr) |
| | file (FI).nm |
| | fprintf (2,'Error:File%s does not exist.Please try it again.\n', file(FI).nm) |
| | fclose (fid) |
| end if | isempty (strfind(file(FI).nm, 'tlrc')) |
| elseif | isempty (strfind(file(FI).nm, 'orig')) |
| else if | isempty (strfind(file(FI).nm, '1D')) |
| | fprintf (2,'Error:format of file%s is incorrect!\n', file(FI).nm) |
| | fprintf (2,'\n factor%c(%s) at level%i(%s),', 64+2, FL(2).expr, jj, FL(2).level(jj).expr) |
| | GP (2, FI) |
| | fprintf (2,'\n factor%c(%s) at level%i(%s),', 64+3, FL(3).expr, kk, FL(3).level(kk).expr) |
| | GP (3, FI) |
| | fprintf (2,'\n factor%c(%s) at level%i(%s),', 64+3, FL(3).expr, kk, FL(4).level(ll).expr) |
| | GP (4, FI) |
| else | fprintf (2,'Error:Total number of files do not match up.\n') |
| end end end | if (dsgn==1) if((NF |
| File index | for (k=1:1:FL(3).UL(i).N_level) |
| while | fprintf (2,'\n(%i) factor combination:\n', FI) |
| | for (m=1:1:NF) |
| | fprintf ('\tfactor%c(%s) at level%s\n', 64+m, FL(m).expr, char(GP(m, FI))) |
| end | fprintf ('\tat repeat%i\n', r) |
| end i end end | if ((NF==3 &dsgn==3)) if((NF |
| File index | for (l=1:1:FL(4).UL(i).N_level) |
| end end end | if ((NF==4 &dsgn==3))%end%(unbalanced.yes |
| while | fprintf (2,'\n(%i) factor combination:\n', i) |
| | fprintf ('\tfactor%c(%s) at level%i(%s)\n', 64+k, FL(k).expr, scpt(k), FL(k).level(scpt(k)).expr) |
| | GP (k, i) |
| end | fprintf ('\tat repeat%i\n', scpt(NF+1)) |
| | file (i).nm |
| | fprintf (2,'Error:File%s does not exist.Please try it again.\n', file(i).nm) |
| end if | isempty (strfind(file(i).nm, 'tlrc')) |
| elseif | isempty (strfind(file(i).nm, 'orig')) |
| else if | isempty (strfind(file(i).nm, '1D')) |
| | fprintf (2,'Error:format of file%s is incorrect!\n', file(i).nm) |
| (NF==4 &dsgn==3 | acc () |
| end | counter (m)=0 = counter(m) + 1 |
| while | fprintf ('Input file for subject#%i ', i) |
| | fprintf ('\tThe corresponding level of factor 1 for subject%i ', i) |
| level for factor | if (isnumeric(file(i).F1L)==0|isempty(file(i).F1L)) |
| end | if (file(i).F1L==m) |
Any better way to implement
this without the temporary
array of | counter (j)?end%set a counter of 4th factor level marker for later use end if(fid = counter(j) + 1 |
| end end end | fprintf ('\nIt is assumed that all files have the same subbrik order.') |
| | fprintf ('\nFor each subbrik of an input file, specify the factor level of 2nd and 3rd factors.\n') |
| | fprintf ('\n\tFor subbrik%i:\n', j-1) |
Here we only keep record of
nd and rd factor levels | fprintf ('\t\tlevel of factor%c(%s) ', 65+k, FL(k+1).expr) |
| | SB (j).lv(k) = input('is: ') |
| | if (fid2~=-1) |
| | fprintf (2,'Error:File%s exists already.Please give another name.\n', OutFN) |
| | if (Contr.do~=0 &Contr.do~=1) |
| | fprintf (2,'Error:invalid answer.Try it again.\n', OutFN) |
| end end | if (Contr.do==0) |
| else | fprintf ('\nNow coding contrasts:\n') |
| | fprintf ('\n\t1.Each contrast should contain at least 2 terms;') |
| | fprintf ('\n\t2.Each term in a contrast should have%i character(s),\n', NF) |
| | fprintf ('\tNo.%i character corresponds to the level of factor%c(%s),\n', i, 'A'+i-1, FL(i).expr) |
| end | fprintf ('\n\tUse 0 if a factor is collapsed.\n') |
| | fprintf ('\n\tIf a factor level is smaller than 9, use its ordinal number;') |
| | fprintf ('\n\tIf a factor level is bigger than 9, use a, b, c,...(no capitals) for 10, 11, 12,...\n') |
| | fprintf ('\n\t3.All weights/coeficients in a contrast have to add up to zero.\n') |
| while | fprintf ('\n1st order contrasts have%i factor(s) collapsed.\n', NF-1) |
| | if (isnumeric(Contr.ord1.tot)==0|Contr.ord1.tot< 0) |
| | fprintf (2,'Error:inapproriate input.Please try again.\n') |
| end end | fprintf ('\nUse factor level to code each term in a contrast.For example, 1 means the factor is at first level.\n') |
| | fprintf ('\nLabel for 1st order contrast No.%i ', i) |
| Contr ord1 | label (i).nm |
| while Contr ord1 | cnt (i).NT |
| | fprintf (2,'\nError:inapproriate input.Please try again.\n\n') |
| while | fprintf ('Factor index for No.%i term ', j) |
| | if (length(Contr.ord1.cnt(i).code(j).str)~=NF) |
| | fprintf (2,'Error:invalid input.Try it again.\n', OutFN) |
| end | if (sum(Contr.ord1.cnt(i).coef)~=0) |
| | fprintf (2,'\nError:All the coeficients of a contrast have to sum up to 0!Try again...\n\n') |
| | fprintf (1,'Done with 1st order contrast information.\n') |
| | fprintf (2,'\nError:inapproriate input.Please try again.\n') |
| | fprintf (2,'\nError:invalid input.Try it again.\n', OutFN) |
| while | fprintf ('\n2nd order contrasts have%i factor(s) collapsed.\n', NF-2) |
| | fprintf ('\nNotice:Contrasts for random factor are NOT feasible.\n') |
| end end | fprintf ('\nUse factor level to code each term in a contrast.For example, 12 means ') |
| | fprintf ('\nthe 1st and 2nd factors are at their first and second level respectively.\n') |
| | fprintf ('\nLabel for 2nd order contrast No.%i: ', i) |
| | if (length(Contr.ord2.cnt(i).code(j).str)~=NF) |
| end | if (sum(Contr.ord2.cnt(i).coef)~=0) |
| | fprintf (1,'Done with 2nd order contrast information.\n') |
| | fprintf ('\t1.Simple mean for a factor level, such as[1 0 0];\n') |
| | fprintf ('\t2.Difference between two factor levels, such as[1-1 0];\n') |
| | fprintf ('\t3.Linear combination of factor levels, such as[0.5 0.5-1];\n') |
| end end | fprintf ('\nUse factor level to code each term in a contrast.For example, 0100 means the first, third ') |
| | fprintf ('\nand fourth factors are collapsed while 2nd factor is at first level.\n') |
| end end | fprintf ('\nUse factor level to code each term in a contrast.For example, 0120 means both the first ') |
| | fprintf ('\nand fourth factors are collapsed while 2nd and 3rd factors are at first and second level respectively.\n') |
| | fprintf ('\nLabel for 2nd order contrast No.%i ', i) |
| while | fprintf ('\n3rd order contrasts have%i factor(s) collapsed.\n', NF-3) |
| end end | fprintf ('\nUse factor level to code each term in a contrast.For example, 1230 means the fourth') |
| | fprintf ('\nfactor is collapsed while all the other 3 factors are at first, second and third level respectively.\n') |
| | fprintf ('\nLabel for 3rd order contrast No.%i ', i) |
| | if (length(Contr.ord3.cnt(i).code(j).str)~=NF) |
| end | if (sum(Contr.ord3.cnt(i).coef)~=0) |
| | fprintf (1,'Done with 3rd order contrast information.\n') |
| while | fprintf ('\n4th order contrasts have%i factor(s) collapsed.\n', NF-4) |
| | fprintf ('\nLabel for 4th order contrast No.%i ', i) |
| | if (length(Contr.ord4.cnt(i).code(j).str)~=NF) |
| end | if (sum(Contr.ord4.cnt(i).coef)~=0) |
| end | fprintf (1,'Done with 4th order contrast information.\n') |
| id | dsgn () |
| end end end | if (i==NF &cov.do) |
| end end end | group (NF) |
Convert the cloumn into one
row | varnames (NF) |
| else | group (i) |
| | varnames (i) |
| id | marker () |
| R | XC () |
| | varnames (2) |
| | varnames (3) = varnames(4) |
| | FL (2) |
| | FL (3) = FL(4) |
| id | group () |
| | varnames (4) |
| | FL (4) |
Get the number of slices along
Z axis from file header | elseif (data_type==1) = '.1D.dset' |
Get the number of slices along
Z axis from file header | if (Frame_N==1) |
| end | fprintf (1, '\nTotal slices along Z axis:%i-You can estimate the total runtime\n', slices) |
| | fprintf (1, '\tby multiplying the runtime for each slice from down below.\n') |
| | fprintf (1, '\nRunning analysis on slice:\n') |
| | for (sn=1:1:slices) |
| | fprintf ('\t#%d... ', sn) |
Each file contains only single
subbrik | fprintf (1,'\nReading%d input files...', ntot) |
| | if (sn~=1) |
| | X (:, 1, i) |
| end | if (err==1) |
| end | fprintf (2,'Error:failure on loading file%s--%s.\n', file(i).nm, ErrMessage) |
end end end end Each file
contains mutliple subbriks
from one subject | fprintf (1,'\nReading slice#%d from%d input files... ', sn, file_num) |
| end Read in each file For each | subject (file) |
end Read in each file For
each there should have | FL (1).N_level *FL(4).N_level files%[err |
end Read in each file For
each there should have | tmp (:,:,:,(i-1)*file_SB+1:i *file_SB) |
| id | order:factor:factor:factor:factor: (id st,[factor] 4 nd,[factor] 4 rd,[factor] 4 th,[factor] 1 DATASET_DIMENSIONS) |
initialization Assemble a
matrix with intensity and
F value sandwiched with each
other | M (i, j, k, 2 *l-1) |
| | M (i, j, 2 *l-1) |
| | M (i, j, k, 2 *l) |
| | M (i, j, 2 *l) |
| end | if (Contr.ord1.tot >0) |
| end | M (i, j, 2 *(l+N_Brik)-1) |
| | M (i, j, 2 *(l+N_Brik)) |
| end end | if (Contr.ord2.tot >0) |
| end end | M (i, j, 2 *(l+N_Brik+Contr.ord1.tot)-1) |
| | M (i, j, 2 *(l+N_Brik+Contr.ord1.tot)) |
| end end | if (Contr.ord3.tot >0) |
| end end | M (i, j, 2 *(l+N_Brik+Contr.ord1.tot+Contr.ord2.tot)-1) |
| | M (i, j, 2 *(l+N_Brik+Contr.ord1.tot+Contr.ord2.tot)) |
| end end | if (Contr.ord4.tot >0) |
| end end | M (i, j, 2 *(l+N_Brik+Contr.ord1.tot+Contr.ord2.tot+Contr.ord3.tot)-1) |
| | M (i, j, 2 *(l+N_Brik+Contr.ord1.tot+Contr.ord2.tot+Contr.ord3.tot)) |
end end end end Get df for
st order contrasts | if ((NF==3|NF==4)&Contr.ord1.tot > 0) |
end end end end Get df for
st order contrasts Contr ord1 | df (i) |
end end Get df for nd order
contrasts | if ((NF==3)&Contr.ord2.tot > 0) |
| MSAC end | if (Contr.ord2.cnt(i).idx2==3) |
| MSBC else | fprintf ('\nSomething is wrong in the contrast coding!\n') |
| end end end | if ((NF==4)&Contr.ord2.tot > 0) |
Less likely switch Contr ord3
switch Contr ord3 | if (Contr.ord3.cnt(i).idx3==3) |
| end end end | if ((NF==4)&Contr.ord3.tot > 0) |
| MSABD not exist | for (dsgn==3|dsgn==4|dsgn==5) end case 3 |
| end end end end | if ((NF==5)&Contr.ord3.tot > 0) |
| | elseif (dsgn==3) |
| | dfdenom (21) |
end MSABCE end switch Contr
ord4 | if (Contr.ord4.cnt(i).idx4==5) |
| Info | DATASET_RANK (2) |
| Label for t end Info | SCENE_DATA (2) |
means Bucket Func defined
in AFNI doc README attributes
Info | SCENE_DATA (3) |
| end | fprintf (1, 'done in%f seconds\n', toc) |
end end of the big loop of
running ANOVA and writing
job is successfully done Total | etime (clock, t0)/60) |
| | fprintf (1, '\nOutput files are%s%s.*\n\n', Opt.Prefix, Opt.View) |
Variables |
| GroupAna m | Purpose |
GroupAna m Bethesda MD Define
the function name for easy
referencing | FuncName = 'GroupAna.m' |
| Debug Flag | DBG = 1 |
| initailize return variables | err = 1 |
| clear | all |
Grouop analysis for Volume
or Surface data | flg = 0 |
| while | data_type = input('\nGroups analysis for volume or surface data (0 - volume; 1 - surface)? ') |
| end end If for surface | data = BrikLoad(file(i).nm, Opt) |
| | Frame_N = input('\nWhich column corresponds to regressor coefficient? (1, 2, 3, ...) ') |
| while | node_n = input('\nHow many number of nodes in the surface data? ') |
| end end else Opt | Frames = 1 |
| while | NF = input('\nHow many factors? ') |
| end end switch NF | case |
| while | dsgn = input('\nChoose design type (1, 2, 3, 4, 5): ') |
| while | slices = input('How many slices along the Z axis (run 3dinfo on one of the input files to find out)? ') |
| while unbalanced | yes = 1 - input('\nIs the design balanced? (1 - Yes; 0 - No) ') |
| | pause |
| unbalanced | type = input('\nChoose design type (1, 2): ') |
| | ntot = 1 |
| Basically | for = Contr.ord2.cnt(i).idx2 |
| | flag = 0 |
| while | combine = [] |
| cov | label = [] |
| while cov | do = input('\nAny covariate (concomitant variable)? (1 - Yes; 0 - No) ') |
| while cov | FN = input('\nConvariate file name: ', 's') |
| | fid0 = fopen(cov.FN,'r') |
| | file_format = input('(1 - Single brik; 0 - Multiple subbriks) ') |
| | file_num = input('Number of input files: ') |
| | file_SB = input('Number of subbriks for analysis in each file: ') |
| | corr = input('Correct? (1 - Yes; 0 - No) ') |
end end end generate the subcripts
and obtain all input files | GP = cell(NF, ntot) |
| | sz = input('\nsample size is: ') |
| | FI = FI + 1 |
| | fid = fopen (file(FI).nm,'r') |
end end end end end end k
end j | acc = FI |
Ziad Saad modified Matlab
function ind2sub for the purpose
here Converting the index
into multiple subscripts I
want vary the levels starting
the last factor in stead of
the | first [err, file(i).v] = gind2sub (fliplr(sz), i) |
flip before subscripting Doing
flip because I want vary the
levels starting the last factor
in stead of the first | scpt = fliplr(file(i).v) |
| while | OutFN = input('\nOutput file name (in bucket format): ', 's') |
| | OutFull = sprintf('%s+%s.HEAD', OutFN, format) |
| | fid2 = fopen(OutFull,'r') |
| end end Gather contrast | information |
| end end Contr ord1 | tot = 0 |
| | NT |
| end end | flg0 = 0 |
end Done with nd order contrast
information | n |
temporary solution when no
covariate exists in PreProc
m new design type after covariate
is | added |
end end swap the covariate
with another factor for some
special | cases |
| | temp1 = group{2} |
| | temp2 = varnames(2) |
| | temp3 = FL(2) |
| cov | marker = 2 |
end end end case end switch
end | N_Brik = 2^NF - 1 |
| For way with crossed | design |
For way with crossed there
are effect | terms |
For way with crossed there
are effect | B |
For way with crossed there
are effect | C |
For way with crossed there
are effect | D |
For way with crossed there
are effect | AB |
For way with crossed there
are effect | AC |
For way with crossed there
are effect | AD |
For way with crossed there
are effect | BC = [msterm(1:4), msterm(6)] |
For way with crossed there
are effect | BD |
For way with crossed there
are effect | ABC |
For way with crossed there
are effect | ABD |
For way with crossed there
are effect | BCD |
| end end Voxel independent | stuff [err, Qd, s, termname, nterms, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Contr] = PreProc(ntot, NF, group, varnames, FL, Contr, cov, unbalanced) |
Use Ziad s function BrikLoad
to load all ntot of datasets
in a column format since matlab
function anovan only accepts
vectors Opt | Format = PreProc(ntot, NF, group, varnames, FL, Contr, dsgn, cov) 'matrix' |
| | t0 = clock |
Get the number of slices along
Z axis from file header Opt | method = 1 |
| end Opt | SliceSize_1D = 50000 |
| | tic |
| Opt | Slices = sn |
| end For the last chunk of | nodes |
end For the last chunk of
which are not a whole set | of |
end For the last chunk of
which are not a whole set
Not an elegant | solution |
end For the last chunk of
which are not a whole set
Not an elegant | i = Z |
| clear | Z |
end Read in each file For
each there should have | Info |
end Read in each file For
each there should have | ErrMessage = BrikLoad(file(i).nm,Opt) |
| end end For each | subbrik |
end end For each there should
have FL(2).N_level *FL(3).N_level subbriks%X(For
each there should have FL(2).N_level *FL(3).N_level
subbriks X(end else | fprintf (2,'Sorry, I cannot handle mutliple subbriks for this case.\n') = AFNI_Index2XYZcontinuous (Indx, Info, 'ILA') |
| X | D2 = Info.DATASET_DIMENSIONS(2) |
| Y | D3 = Info.DATASET_DIMENSIONS(3) |
| Z | dim = size(X) |
| | fstat = zeros(D1, D2, D3, N_Brik) |
| | intensity = zeros(D1, D2, D3, N_Brik) |
| | Y = reshape(X, ntot, D1, D2) |
Have not figured out how to
change the shape of the matrix
yet end end | end |
| initialization | M = zeros(D1, D2, 2*(N_Brik+Contr.ord1.tot+Contr.ord2.tot+Contr.ord3.tot+1)) |
| Less likely | occur |
end df of MSE Set up options
for writing out the results
Opt | Prefix = sprintf('%s', OutFN) |
| Opt | NoCheck = 0 |
| Opt | Scale = 1 |
| Opt | View = sprintf('+%s', format) |
| end Info | TYPESTRING = '3DIM_HEAD_FUNC' |
| Number of subbriks Info | DATASET_DIMENSIONS = [D1 D2 D3 0 0] |
| Info | BRICK_STATS = [] |
| Info | BRICK_TYPES = [] |
| Info | BRICK_FLOAT_FACS = [] |
| Info | BRICK_STATAUX = [] |
| initialization | __pad1__ |
| for | float |
for short end For all terms
Info | BRICK_LABS = [] |
| means | DIM_HEAD_FUNC |
Because it might have been
set as the frame list in the
case of input files with multiple
subbriks during loading Write | output |
Because it might have been
set as the frame list in the
case of input files with multiple
subbriks during loading Write
Collapse the nd | dimsion |
end end of the big loop of
running ANOVA and writing | up |
end end of the big loop of
running ANOVA and writing | nCongratulations |
end end of the big loop of
running ANOVA and writing
job is successfully done Total | runtime |
| | return |
Function Documentation
| (NF == 4 & dsgn == 3 acc |
( |
|
) |
[virtual] |
|
| id ANCOVA: |
( |
'\nLabel for No.%i ' |
, |
|
|
i |
fprintf |
|
) |
[virtual] |
|
| while Contr ord1 cnt |
( |
i |
|
) |
|
|
| Any better way to implement this without the temporary array of counter |
( |
j |
|
) |
= counter(j) + 1 |
|
| end counter |
( |
m |
|
) |
= counter(m) + 1 [pure virtual] |
|
| elseif |
( |
length(unique(combine)) |
= = sum([FL(NF).UL(:).N_level]) |
) |
|
|
| end end of the big loop of running ANOVA and writing job is successfully done Total etime |
( |
clock |
, |
|
|
t0 |
|
|
) |
|
|
| dsgn == 1 FI |
( |
|
) |
[virtual] |
|
| end Read in each file For each there should have FL |
( |
1 |
|
) |
|
|
| FL |
( |
i |
|
) |
= input('have? ') |
|
| MSABD not exist for |
( |
dsgn |
= = 3 | dsgn == 4 | dsgn == 5 |
) |
|
|
| File index for |
( |
l |
= 1:1:FL(4).UL(i).N_level |
) |
|
|
| File index for |
( |
k |
= 1:1:FL(3).UL(i).N_level |
) |
|
|
| end for |
( |
j |
= 1:1:FL(i).N_level |
) |
|
|
| end end for |
( |
ii |
= 1:1:5 |
) |
[pure virtual] |
|
| fprintf |
( |
1 |
, |
|
|
'\nOutput files are%s%s.*\n\n' |
, |
|
|
Opt. |
Prefix, |
|
|
Opt. |
View |
|
) |
|
|
| end fprintf |
( |
1 |
, |
|
|
'done in%f seconds\n' |
, |
|
|
toc |
|
|
) |
|
|
| end fprintf |
( |
2 |
, |
|
|
'Error:failure on loading file%s--%s.\n' |
, |
|
|
file(i). |
nm, |
|
|
ErrMessage |
|
|
) |
|
|
| fprintf |
( |
'\t#%d... ' |
, |
|
|
sn |
|
|
) |
|
|
| fprintf |
( |
1 |
, |
|
|
'\nRunning analysis on slice:\n' |
|
|
) |
|
|
| fprintf |
( |
'\nfactor is collapsed while all the other 3 factors are at |
first, |
|
|
second and third level respectively.\n' |
|
|
) |
|
|
| end end fprintf |
( |
'\nUse factor level to code each term in a contrast.For |
example, |
|
|
1230 means the fourth' |
|
|
) |
|
|
| fprintf |
( |
'\nand fourth factors are collapsed while 2nd and 3rd factors are at first and second level respectively.\n' |
|
) |
|
|
| end end fprintf |
( |
'\nUse factor level to code each term in a contrast.For |
example, |
|
|
0120 means both the first ' |
|
|
) |
|
|
| fprintf |
( |
'\nand fourth factors are collapsed while 2nd factor is at first level.\n' |
|
) |
|
|
| end end fprintf |
( |
'\nUse factor level to code each term in a contrast.For |
example, |
|
|
0100 means the |
first, |
|
|
third ' |
|
|
) |
|
|
| fprintf |
( |
'\t3.Linear combination of factor |
levels, |
|
|
such as;\n' |
[0.5 0.5-1] |
|
) |
|
|
| fprintf |
( |
'\t2.Difference between two factor |
levels, |
|
|
such as;\n' |
[1-1 0] |
|
) |
|
|
| fprintf |
( |
'\t1.Simple mean for a factor |
level, |
|
|
such as;\n' |
[1 0 0] |
|
) |
|
|
| fprintf |
( |
'\nthe 1st and 2nd factors are at their first and second level respectively.\n' |
|
) |
|
|
| end end fprintf |
( |
'\nUse factor level to code each term in a contrast.For |
example, |
|
|
12 means ' |
|
|
) |
|
|
| fprintf |
( |
'\nNotice:Contrasts for random factor are NOT feasible.\n' |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\nError:invalid input.Try it again.\n' |
, |
|
|
OutFN |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\nError:inapproriate input.Please try again.\n' |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:invalid input.Try it again.\n' |
, |
|
|
OutFN |
|
|
) |
|
|
| while fprintf |
( |
'Factor index for No.%i term ' |
, |
|
|
j |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\nError:inapproriate input.Please try again.\n\n' |
|
|
) |
|
|
| end end fprintf |
( |
'\nUse factor level to code each term in a contrast.For |
example, |
|
|
1 means the factor is at first level.\n' |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:inapproriate input.Please try again.\n' |
|
|
) |
|
|
| fprintf |
( |
'\n\t3.All weights/coeficients in a contrast have to add up to zero.\n' |
|
) |
|
|
| fprintf |
( |
'\n\tIf a factor level is bigger than |
9, |
|
|
use |
a, |
|
|
b |
, |
|
|
c |
, |
|
|
...(no capitals) for |
10, |
|
|
11 |
, |
|
|
12 |
, |
|
|
...\n' |
|
|
) |
|
|
| fprintf |
( |
'\n\tIf a factor level is smaller than |
9, |
|
|
use its ordinal number;' |
|
|
) |
|
|
| end fprintf |
( |
'\n\tUse 0 if a factor is collapsed.\n' |
|
) |
|
|
| fprintf |
( |
'\tNo.%i character corresponds to the level of factor% |
c(%s), |
|
|
\n' |
, |
|
|
i |
, |
|
|
'A'+i- |
1, |
|
|
FL(i). |
expr |
|
) |
|
|
| fprintf |
( |
'\n\t2.Each term in a contrast should have%i |
character(s), |
|
|
\n' |
, |
|
|
NF |
|
|
) |
|
|
| else fprintf |
( |
'\nNow coding contrasts:\n' |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:invalid answer.Try it again.\n' |
, |
|
|
OutFN |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:File%s exists already.Please give another name.\n' |
, |
|
|
OutFN |
|
|
) |
|
|
| Here we only keep record of nd and rd factor levels fprintf |
( |
'\t\tlevel of factor%c(%s) ' |
, |
|
|
65+ |
k, |
|
|
FL(k+1). |
expr |
|
) |
|
|
| fprintf |
( |
'\tThe corresponding level of factor 1 for subject%i ' |
, |
|
|
i |
|
|
) |
|
|
| while fprintf |
( |
'Input file for subject#%i ' |
, |
|
|
i |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:format of file%s is incorrect!\n' |
, |
|
|
file(i). |
nm |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:File%s does not exist.Please try it again.\n' |
, |
|
|
file(i). |
nm |
|
) |
|
|
| fprintf |
( |
'\tfactor%c(%s) at level%i(%s)\n' |
, |
|
|
64+ |
k, |
|
|
FL(k). |
expr, |
|
|
scpt(k) |
, |
|
|
FL(k).level(scpt(k)). |
expr |
|
) |
|
|
| while fprintf |
( |
2 |
, |
|
|
'\n(%i) factor combination:\n' |
, |
|
|
i |
|
|
) |
|
|
| end fprintf |
( |
'\tat repeat%i\n' |
, |
|
|
r |
|
|
) |
|
|
| fprintf |
( |
'\tfactor%c(%s) at level%s\n' |
, |
|
|
64+ |
m, |
|
|
FL(m). |
expr, |
|
|
char(GP(m, FI)) |
|
|
) |
|
|
| while fprintf |
( |
2 |
, |
|
|
'\n(%i) factor combination:\n' |
, |
|
|
FI |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\n factor% |
c(%s) at level%i(%s), |
|
|
' |
, |
|
|
64+ |
3, |
|
|
FL(3). |
expr, |
|
|
kk |
, |
|
|
FL(4).level(ll). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\n factor% |
c(%s) at level%i(%s), |
|
|
' |
, |
|
|
64+ |
3, |
|
|
FL(3). |
expr, |
|
|
kk |
, |
|
|
FL(3).level(kk). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\n factor% |
c(%s) at level%i(%s), |
|
|
' |
, |
|
|
64+ |
2, |
|
|
FL(2). |
expr, |
|
|
jj |
, |
|
|
FL(2).level(jj). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:format of file%s is incorrect!\n' |
, |
|
|
file(FI). |
nm |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:File%s does not exist.Please try it again.\n' |
, |
|
|
file(FI). |
nm |
|
) |
|
|
| while fprintf |
( |
2 |
, |
|
|
'No.%i file ' |
, |
|
|
rr |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\nProvide those%i input files:\n' |
, |
|
|
sz |
|
|
) |
|
|
| end switch NF fprintf |
( |
2 |
, |
|
|
'\nFor factor% |
c(%s) at level%i(%s), |
|
|
' |
, |
|
|
64+ |
1, |
|
|
FL(1). |
expr, |
|
|
ii |
, |
|
|
FL(1).level(ii). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:Check the inconsistency.\n' |
|
|
) |
|
|
| end fprintf |
( |
2 |
, |
|
|
'\nError:The number of files and subbriks are not consistent!\n' |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:File%s does not exist.Please try it again.\n' |
, |
|
|
cov. |
FN |
|
) |
|
|
| '\nThe 2-way ANCOVA for this design is currently NOT available.\n' fprintf |
( |
|
) |
[virtual] |
|
| fprintf |
( |
2 |
, |
|
|
'\nError:There is some overlap among the labels of factor%c(%s) across the groups of factor%c(%s)!\n' |
, |
|
|
...64+ |
NF, |
|
|
FL(NF). |
expr, |
|
|
64+ |
1, |
|
|
FL(1). |
expr |
|
) |
|
|
| unbalanced levels for this factor fprintf |
( |
'Label for No.%i level of factor%c(%s) in group%i of factor%c(%s)' |
, |
|
|
j |
, |
|
|
64+ |
NF, |
|
|
FL(NF). |
expr, |
|
|
i |
, |
|
|
64+ |
1, |
|
|
FL(1). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'How many levels does factor%c(%s) corresponding to level%i(%s) of factor%c(%s) ' |
, |
|
|
...64+ |
NF, |
|
|
FL(NF). |
expr, |
|
|
i |
, |
|
|
FL(1).level(i). |
expr, |
|
|
64+ |
1, |
|
|
FL(1). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\nhas to be DIFFERENT for each level of factor%c(%s)!!!\n\n' |
, |
|
|
64+ |
1, |
|
|
FL(1). |
expr |
|
) |
|
|
| Label this unbalanced factor fprintf |
( |
2 |
, |
|
|
'\nNote:Since this is a nested design the label for levels(usuall subject names) of factor No.%i(%c-%s)' |
, |
|
|
NF |
, |
|
|
64+ |
NF, |
|
|
FL(NF). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'\nLabel for No.%i ' |
, |
|
|
NF |
|
|
) |
|
|
| total number of combinations end end fprintf |
( |
'\nLabel for No.%i ' |
, |
|
|
i |
|
|
) |
|
|
| end fprintf |
( |
'Label for No.%i level of factor%c(%s)' |
, |
|
|
j |
, |
|
|
64+ |
i, |
|
|
FL(i). |
expr |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:the input is not a number.Please try again.\n' |
|
|
) |
|
|
| Factor Label i fprintf |
( |
2 |
, |
|
|
'How many levels does factor%c(%s) ' |
, |
|
|
64+ |
i, |
|
|
FL(i). |
expr |
|
) |
|
|
| fprintf |
( |
'\n\t For |
example, |
|
|
add somethint here later...\n' |
|
|
) |
|
|
| fprintf |
( |
'\nType 2:Not type |
1, |
|
|
but there are different sample sizes for some cells(factor level combinations).' |
|
|
) |
|
|
| fprintf |
( |
'\n\t there can be different number of subjects for each level of factor A;\n' |
|
) |
|
|
| fprintf |
( |
'\nType 1:When subject is a random factor and nested within another |
factor(3-way ANOVA type 3, 4-way ANOVA types 3 and 5), |
|
|
' |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Halted:Ctrl+c to exit' |
|
|
) |
|
|
| fprintf |
( |
'\n\t 3-way ANOVA type 3:BXC(A);and 4-way ANOVA type 3:BXCXD(A)' |
|
) |
|
|
| fprintf |
( |
'\n\t each level of factor A contains a unique and unequal number of subjects- ' |
|
) |
|
|
| fprintf |
( |
'\n\n(2) When a random factor(subject) is nested within another factor |
A, |
|
|
' |
|
|
) |
|
|
| fprintf |
( |
'\n\t 1-way ANOVA;2-way ANOVA type 1:AXB;and 3-way ANOVA type 1:AXBXC' |
|
) |
|
|
| end fprintf |
( |
'\nThe following two kinds of unbalanced designs are currently allowed:\n' |
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:inapproriate input.Please try it again.\n' |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:input is not a number.Please try it again.\n' |
|
|
) |
|
|
| fprintf |
( |
'\n\t is random.\n' |
|
) |
|
|
| fprintf |
( |
'\n\tType 4:Mixed design BXCXDXE(A)-the 5th factor E is nested within factor |
A, |
|
|
but factor D(usually subject)' |
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|
) |
|
|
| fprintf |
( |
'\n\t Also called 4-way design with factors |
B, |
|
|
C and D varying within subject and factor A between subjects.\n' |
|
|
) |
|
|
| fprintf |
( |
'\n\tType 3:Mixed design BXCXDXE(A)-only the nested(5th) factor E(usually subject) is random.' |
|
) |
|
|
| fprintf |
( |
'\n\t called 4-way design with all 4 factors |
A, |
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|
B |
, |
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C and D varying within subject.\n' |
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|
) |
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| fprintf |
( |
'\n\tType 2:Factorial(crossed) design AXBXCXDXE-only factor E is random.If E is subject it is also' |
|
) |
|
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| fprintf |
( |
'\n\tType 1:Factorial(crossed) design AXBXCXDXE-all 5 factors are fixed.\n' |
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) |
|
|
| fprintf |
( |
'\nNotice:This is NOT an exhaustive list of design types for 4-way ANOVA.Other types might be implemented upon request.\n' |
|
) |
|
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| fprintf |
( |
'\n\t design with factor D varying within-subject and factors A and B between-subjects.\n' |
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) |
|
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| fprintf |
( |
'\n\t but factor D is nested within both factors A and B.If D is subject it is also called 3-way' |
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) |
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| fprintf |
( |
'\n\tType 5:Mixed design CXD(AXB)-only the nested(4th) factor D(usually subject) is |
random, |
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|
' |
|
|
) |
|
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| fprintf |
( |
'\n\t is random.' |
|
) |
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| fprintf |
( |
'\n\t Also called 3-way design with factors B and C varying within subject and factor A between subjects.' |
|
) |
|
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| fprintf |
( |
'\n\tType 3:Mixed design BXCXD(A)-only the nested(4th) factor D(usually subject) is random.' |
|
) |
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| fprintf |
( |
'\n\t called 3-way design with all 3 factors |
A, |
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B |
, |
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and C varying within subject.' |
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) |
|
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| fprintf |
( |
'\n\tType 2:Factorial(crossed) design AXBXCXD-only factor D is random.If D is subject it is also' |
|
) |
|
|
| fprintf |
( |
'\n\tType 1:Factorial(crossed) design AXBXCXD-all 4 factors are fixed.\n' |
|
) |
|
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| fprintf |
( |
'\n\tType 4:Mixed design BXC(A)-Fixed factor C is nested within fixed factor A while B(usually subject) is random.\n' |
|
) |
|
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| fprintf |
( |
'\n\tType 3:Mixed design BXC(A)-A and B are fixed while C(usually subject) is random and nested within A.\n' |
|
) |
|
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| fprintf |
( |
'\n\t run any constrast tests including mean estimates and differences for factor C with this design type.\n' |
|
) |
|
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| fprintf |
( |
'\n\t usually called 2-way design with A and B varying within subject.Notice:It is inappropriate to' |
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) |
|
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| fprintf |
( |
'\n\tType 2:Factorial(crossed) design AXBXC-factors A and B are fixed while C is random.If C is |
subject, |
|
|
it is' |
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|
) |
|
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| fprintf |
( |
'\n\tType 1:Factorial(crossed) design AXBXC-all factors are fixed.\n' |
|
) |
|
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| fprintf |
( |
'\n\tType 3:Factorial(crossed) design AXB-both factors are random.\n' |
|
) |
|
|
| fprintf |
( |
'\n\t run any constrasts including mean estimates and differences for factor B with this design type.\n' |
|
) |
|
|
| fprintf |
( |
'\n\t usually called 1-way design with A varying within subject.Notice:It is inappropriate to' |
|
) |
|
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| fprintf |
( |
'\n\tType 2:Factorial(crossed) design AXB-factor A is fixed while B is random.If B is |
subject, |
|
|
it is' |
|
|
) |
|
|
| fprintf |
( |
'\n\tType 1:Factorial(crossed) design AXB-both factors are fixed.\n' |
|
) |
|
|
| fprintf |
( |
'\nAvailabe design types:\n' |
|
) |
|
|
| fprintf |
( |
'\n\tType 1:one factor with fixed effect.\n' |
|
) |
|
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| fprintf |
( |
2 |
, |
|
|
'Error:the input is not a number.Please try it again.\n' |
|
|
) |
|
|
| fprintf |
( |
1 |
, |
|
|
'\nProgram @Purify_1D can be used to extract the regressor coefficient column to a 1D file.' |
|
|
) |
|
|
| fprintf |
( |
2 |
, |
|
|
'Error:wrong input!Please try it again.\n' |
|
|
) |
|
|
| fprintf |
( |
'\n\t5.Currently all of the following terms are modeled:main effects and applicable interactions in various |
orders, |
|
|
.\n' |
|
|
) |
|
|
| fprintf |
( |
'\t named by reflecting the hierarchy of the experiment design.\n' |
|
) |
|
|
| fprintf |
( |
'\n\t4.Each input file should include only one subbrik.We suggest files be\n' |
|
) |
|
|
| fprintf |
( |
'\n\t3.With |
nesting, |
|
|
arrange your design in such a way that the last factor is nested within the 1st factor.\n' |
|
|
) |
|
|
| fprintf |
( |
'\t so that subbrik labels can be shown on AFNI viewer.\n' |
|
) |
|
|
| fprintf |
( |
'\n\t2.We strongly suggest that factor names be labeled with short(2 or 3 capital letters) names\n' |
|
) |
|
|
| fprintf |
( |
'\t"the command adwarp -dxyz n"to greatly reduce runtime without sacrificing accuracy.\n' |
|
) |
|
|
| fprintf |
( |
'\n\t1.If the resolution of your EPI data is near n |
millimeters, |
|
|
during Talairach conversion use\n' |
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|
) |
|
|
| save all subsequent command window input and most of the resulting command window output to be appended to file diary fprintf |
( |
'\nPlease read the following carefully about group analysis setup:\n' |
|
) |
|
|
| end switch Contr ord4 switch Contr ord4 switch Contr ord4 if |
( |
Contr.ord4.cnt(i). |
idx4 = = 5 |
) |
|
|
| end end switch Contr ord3 if |
( |
Contr.ord3.cnt(i). |
idx2 = = 3 |
) |
|
|
| MSAC end if |
( |
Contr.ord2.cnt(i). |
idx2 = = 3 |
) |
|
|
| ABCDE if |
( |
Contr.ord2. |
tot, |
|
|
0 |
|
|
) |
|
|
| end if |
( |
sum(Contr.ord4.cnt(i).coef)~ |
= 0 |
) |
|
|
| if |
( |
length(Contr.ord4.cnt(i).code(j).str)~ |
= NF |
) |
|
|
| end if |
( |
sum(Contr.ord3.cnt(i).coef)~ |
= 0 |
) |
|
|
| if |
( |
length(Contr.ord3.cnt(i).code(j).str)~ |
= NF |
) |
|
|
| end if |
( |
sum(Contr.ord2.cnt(i).coef)~ |
= 0 |
) |
|
|
| if |
( |
length(Contr.ord2.cnt(i).code(j).str)~ |
= NF |
) |
|
|
| end if |
( |
sum(Contr.ord1.cnt(i).coef)~ |
= 0 |
) |
|
|
| if |
( |
length(Contr.ord1.cnt(i).code(j).str)~ |
= NF |
) |
|
|
| end end if |
( |
Contr. |
do = = 0 |
) |
|
|
| end if |
( |
file(i). |
F1L = = m |
) |
|
|
| level for factor if |
( |
isnumeric(file(i).F1L) |
= = 0 | isempty(file(i).F1L) |
) |
|
|
|
|
Initial value: = 1),
else
for (i=1:1:ntot),
|
| end switch Contr ord4 switch Contr ord4 switch Contr ord4 if |
( |
dsgn |
= =1 |
) |
|
|
| if |
( |
isnumeric(ntot) |
= = 0 | isempty(ntot) |
) |
|
|
| if |
( |
count~ |
= ntot & ~((NF ==1 | NF == 2 | NF == 3) & dsgn == 1) |
) |
|
|
| Label for t end end ANOCVA if |
( |
cov. |
do = = 1 |
) |
|
|
| if |
( |
isnumeric(FL(i).N_level) |
= = 0 | isempty(FL(i).N_level) |
) |
|
|
| if |
( |
(NF==1|NF==2|NF==3|NF==4)& |
dsgn = = 1 |
) |
|
|
| end if |
( |
unbalanced. |
yes = = 1 |
) |
|
|
| if |
( |
isnumeric(dsgn) |
= = 0 | isempty(dsgn) |
) |
|
|
| if |
( |
isnumeric(NF) |
= = 0 | isempty(NF) |
) |
|
|
| else if isempty |
( |
strfind(file(i).nm, '1D') |
|
) |
|
|
| elseif isempty |
( |
strfind(file(i).nm, 'orig') |
|
) |
|
|
| end if isempty |
( |
strfind(file(i).nm, 'tlrc') |
|
) |
|
|
| else if isempty |
( |
strfind(file(FI).nm, '1D') |
|
) |
|
|
|
|
Initial value: = 0 % if 1D file (surface data)
format = '1D'
|
| elseif isempty |
( |
strfind(file(FI).nm, 'orig') |
|
) |
|
|
| end if isempty |
( |
strfind(file(FI).nm, 'tlrc') |
|
) |
|
|
| M |
( |
i |
, |
|
|
j |
, |
|
|
2 * |
(l+N_Brik+Contr.ord1.tot+Contr.ord2.tot+Contr.ord3.tot) |
|
) |
|
|
| M |
( |
i |
, |
|
|
j |
, |
|
|
2 * |
(l+N_Brik+Contr.ord1.tot+Contr.ord2.tot) |
|
) |
|
|
| M |
( |
i |
, |
|
|
j |
, |
|
|
2 * |
(l+N_Brik+Contr.ord1.tot) |
|
) |
|
|
| M |
( |
i |
, |
|
|
j |
, |
|
|
2 * |
(l+N_Brik) |
|
) |
|
|
| initialization Assemble a matrix with intensity and F value sandwiched with each other M |
( |
i |
, |
|
|
j |
, |
|
|
k |
, |
|
|
2 *l- |
1 |
|
) |
|
|
| id order:factor:factor:factor:factor: |
( |
id |
st, |
|
|
[factor] 4 |
nd, |
|
|
[factor] 4 |
rd, |
|
|
[factor] 4 |
th, |
|
|
[factor] 1 |
DATASET_DIMENSIONS |
|
) |
[virtual] |
|
| means Bucket Func defined in AFNI doc README attributes Info SCENE_DATA |
( |
3 |
|
) |
|
|
| Label for t end Info SCENE_DATA |
( |
2 |
|
) |
|
|
| end Read in each file For each subject |
( |
file |
|
) |
|
|
| total number of factor combinations including repeats sz |
( |
NF+ |
1 |
) |
|
|
| end Read in each file For each there should have tmp |
( |
: |
, |
|
|
: |
, |
|
|
: |
, |
|
|
(i-1)*file_SB+1:i * |
file_SB |
|
) |
|
|
| varnames |
( |
3 |
|
) |
= varnames(4) |
|
| Convert the cloumn into one row varnames |
( |
NF |
|
) |
|
|
Variable Documentation
| For way with crossed there are effect AB |
|
| For way with crossed there are effect ABC |
|
| Throw out those four which do not exist for ABD |
|
| For way with crossed there are effect AC |
|
| For way with crossed there are effect B |
|
| For way with crossed there are effect BCD |
|
| Throw out those four which do not exist for BD |
|
| Info BRICK_FLOAT_FACS = [] |
|
| For way with crossed there are effect C |
|
| For way with crossed there are effect D |
|
|
|
Initial value: SumsOfSquares(reshape(X(i, j, k, :), ntot, 1), ...
% nterms, Qd, s, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Nest) SumsOfSquares(reshape(X(i, j, :), ntot, 1), ...
NF, FL, ntot, nterms, Qd, s, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, dsgn, N_Brik, Contr)===================================
%M = zeros(D1, D2, D3, 2*N_Brik)
Definition at line 1645 of file GroupAna.m. |
| Ziad Saad modified Matlab function ind2sub for the purpose here Converting the index into multiple subscripts I want vary the levels starting the last factor in stead of the first[err, file(i).v] = gind2sub (fliplr(sz), i) |
|
|
|
Definition at line 2019 of file GroupAna.m.
Referenced by AffineBruteForceRender(), AFNI_fimmer_compute(), AFNI_func_overlay(), AFNI_splashup(), alloc_output_mem(), allocate2D(), basis_parser(), break_into_pieces(), calc_sse(), calc_stat(), calculate_results(), check_fill_seq(), checkSpatialActivity(), cl1_solve(), cl1_solve_res(), compact_results(), CompositeSlice(), ComputeWeights(), CorrectOpacity(), CORREL_main(), create_row(), csfft_nextup(), DC_IRF(), DELAY_tsfuncV2(), detrend(), draw_marker(), DrawSubWindow(), EDIT_dset_items(), EDIT_main(), EstimateSecondsPerBFrame(), EstimateSecondsPerIFrame(), EstimateSecondsPerPFrame(), eval_registration(), evaluate_irc(), evaluate_span(), F2D_chainfunc(), fft(), FFT_selection(), fill_seq(), filter(), fim3d_fimmer_compute(), Fourier_Filter_Driver(), get_fft_mag(), get_linear_trend(), get_octant_clips(), get_options(), get_popup_label(), get_quadratic_trend(), HandleEvent(), hilbertdelay_V2(), ifft(), ISQ_cropper(), ISQ_make_montage(), ISQ_mapxy(), ISQ_process_mri(), linear_reg(), load_rect_str(), main(), main_FD_EPI(), MASKAVE_main(), MCW_erode_clusters(), MCW_inverse_histogram_sh(), mean_array(), mri_automask_imarr(), mri_brainormalize(), mri_datum_size(), mri_new_7D_generic(), mri_percents(), mri_psinv(), mri_read_3D(), mri_read_3D_delay(), mri_resize(), mri_resize_NN(), mri_warp3D_align_setup(), mri_warp3D_get_delta(), mri_warp3D_resize(), nctypelen(), ncx_get_double_float(), ncx_put_float_double(), ncx_put_float_int(), ncx_put_float_long(), ncx_put_float_schar(), ncx_put_float_short(), ncx_put_float_uchar(), neighborCount(), NI_text_to_val(), output_results(), pcalc(), PCOR_UPDATE(), PERMTEST_compute(), plot_graphs(), plotpak_getset(), PLUTO_histoplot(), POWER_main(), proc_finalize_shm_volumes(), punwrap(), Put_image(), put_one_arg(), qh_check_points(), read_input_data(), read_socket(), REORDER_main(), ResampleUchar(), ResampleUshort(), rfft(), RT_fim_recurse(), segment_envelope(), segment_imarr(), SER_setup_stuff(), set_color_memplot(), setup_basic_types(), ShadeRawVolume(), ShadeSlice(), ShowIFrameSummary(), ShowPFrameSummary(), ShowRemainingTime(), Smooth_line(), StartMasterServer(), SUMA_AddToBrushStroke(), SUMA_allocate2D(), SUMA_BrainVoyager_Read(), SUMA_Build_Cluster_From_Node(), SUMA_cb_set_threshold(), SUMA_cmap_wid_input(), SUMA_Col2Float(), SUMA_divEdge(), SUMA_DrawLineAxis(), SUMA_DrawROI_NewValue(), SUMA_DsetCol2Float(), SUMA_Engine(), SUMA_EquateSurfaceSize(), SUMA_FindClusters(), SUMA_FormAfnidset(), SUMA_FreeSurfer_Read_eng(), SUMA_input(), SUMA_Interpret_AFNIColor(), SUMA_iRGB_to_OverlayPointer(), SUMA_LatestVersionNumber(), SUMA_Make_Edge_List_eng(), SUMA_MapSurface(), SUMA_Mesh_Area(), SUMA_MT_intersect_triangle(), SUMA_MT_isIntersect_Triangle(), SUMA_NewAreaAtRadius(), SUMA_NewVolumeAtRadius(), SUMA_OpenDrawnROI_1D(), SUMA_OpenDX_Read_CruiseVolHead(), SUMA_PolySurf3(), SUMA_read_ppm(), SUMA_ScaleToMap(), SUMA_ScaleToMap_alaAFNI(), SUMA_SetConvexityPlaneDefaults(), SUMA_SetScaleRange(), SUMA_SphereQuality(), SUMA_StretchToFitLeCerveau(), SUMA_StringToNum(), SUMA_Surface_Curvature(), SUMA_SurfGridIntersect(), SUMA_SwitchState(), SUMA_Taubin_Smooth(), SUMA_Taubin_Smooth_TransferFunc(), SUMA_ThreshVal2ScalePos(), SUMA_triangulateRow(), SUMA_UpdateRotaCenter(), SUMA_UpdateViewPoint(), SYM_expand_ranges(), t_getn_float_double(), THD_3dim_from_block(), THD_add_bricks(), THD_extract_many_series(), THD_get_voxel(), THD_load_ctfmri(), THD_makemask(), updateRateControl(), upsample_1(), upsample_7(), vertex_load(), VPCompAC00G(), VPCompAC11B(), VPCompAC1NB(), VPCompAC1NS(), VPCompAC1PB(), VPCompAC31B(), VPCompAC32B(), VPCompAC3NB(), VPCompAC3NS(), VPCompAC3PB(), VPCompAR00G(), VPCompAR11B(), VPCompAR1NB(), VPCompAR1NS(), VPCompAR1PB(), VPCompAR31B(), VPCompAR32B(), VPCompAR3NB(), VPCompAR3NS(), VPCompAR3PB(), vpRamp(), VPRenderAffine(), VPWarpA101N(), VPWarpA111N(), VPWarpA301N(), VPWarpA331N(), VPWarpA331R(), and write_data_to_file(). |
| while cov FN = input('\nConvariate file name: ', 's') |
|
|
|
Definition at line 330 of file GroupAna.m.
Referenced by SUMA_Build_FirstNeighb(), SUMA_CalcNeighbDist(), SUMA_Chung_Smooth(), SUMA_Chung_Smooth_Weights(), SUMA_Convexity(), SUMA_Convexity_Engine(), SUMA_FillToMask_Engine(), SUMA_FillToMask_Engine_old(), SUMA_Free_FirstNeighb(), SUMA_getoffsets(), SUMA_getoffsets2(), SUMA_getoffsets_ll(), SUMA_inNodeNeighb(), SUMA_Show_SureFit(), SUMA_SureFit_Read_Topo(), SUMA_SureFit_Write(), SUMA_Surface_Curvature(), SUMA_SurfaceObject_Info(), and SUMA_Taubin_Smooth(). |
| for = Contr.ord2.cnt(i).idx2 |
|
|
|
Referenced by glob3(), globextend(), globfree(), merge_frame_interval(), put_sub_image_colormap(), SUMA_AdvancePastNumbers(), SUMA_Align_to_VolPar(), SUMA_Alloc_Generic_Prog_Options_Struct(), SUMA_BrushStrokeToNodeStroke(), SUMA_ClusterCenterofMass(), SUMA_CreateGenericArgParse(), SUMA_GetM2M_NN(), and SUMA_ParseFname(). |
| Use Ziad s function BrikLoad to load all ntot of datasets in a column format since matlab function anovan only accepts vectors Opt Format = PreProc(ntot, NF, group, varnames, FL, Contr, dsgn, cov) 'matrix' |
|
| fprintf = AFNI_Index2XYZcontinuous (Indx, Info, 'ILA') |
|
|
|
Referenced by __glutFatalError(), __glutFatalUsage(), __glutWarning(), _getopt_internal(), add_dataset_list_to_PLUGIN_interface(), add_dataset_to_PLUGIN_interface(), add_extra_color(), add_number_to_PLUGIN_interface(), add_option_to_PLUGIN_interface(), add_overlaycolor_to_PLUGIN_interface(), add_string_to_PLUGIN_interface(), add_timeseries_to_PLUGIN_interface(), add_to_flist(), add_to_string_list(), adjtoklen(), adjust_endpts(), adwarp_refashion_dataset(), AFNI_3d_linefill(), AFNI_do_many_writes(), AFNI_drive_open_graph_1D(), AFNI_drive_open_graph_xy(), AFNI_drive_quit(), AFNI_fimmer_compute(), AFNI_finalize_read_Web_CB(), AFNI_finalize_saveim_CB(), AFNI_finalize_write_palette_CB(), AFNI_finalsave_layout_CB(), AFNI_force_adoption(), AFNI_get_xhair_node(), AFNI_initialize_controller(), afni_io(), AFNI_load_defaults(), AFNI_logger(), AFNI_make_voxwarp(), AFNI_niml_redisplay_CB(), AFNI_niml_workproc(), AFNI_parse_args(), AFNI_plugout_exit(), AFNI_plugout_workproc(), AFNI_process_drawing(), AFNI_process_NIML_data(), AFNI_process_plugout(), AFNI_process_setup(), AFNI_read_images(), AFNI_read_inputs(), AFNI_receive_init(), AFNI_refashion_dataset(), AFNI_rescan_session_NEW(), AFNI_rescan_session_OLD(), AFNI_send_image(), AFNI_setup_viewing(), AFNI_sigfunc(), AFNI_slice_flip(), AFNI_splashup(), AFNI_start_io(), AFNI_start_version_check(), AFNI_startup_layout_CB(), AFNI_startup_timeout_CB(), AFNI_version_check(), afni_vol2surf(), AFNI_vol2surf_func_overlay(), all_mappable_surfs(), alloc_ints(), alloc_output_mem(), alloc_vals_list(), alloc_x_im(), AlphaSim_error(), AREN_render(), AREN_set_graybrick(), AREN_set_opabrick(), AREN_set_rgbbricks(), AREN_set_size(), AREN_set_viewpoint(), arg_verify(), argscale(), argverify(), ART_exit(), ART_open_afni_link(), ART_send_control_info(), ART_send_end_of_run(), ART_send_volume(), ART_start_io(), ascii_get_element(), atr_print(), AV_textact_CB(), avg_epochs(), AW_error(), B2F_read_opts(), bad_type(), badBGLengths(), badBlockHeader(), badchar(), badflag(), basis_parser(), basis_write_iresp(), basis_write_sresp(), beep_CB(), betasolve(), BFIT_compute(), BFIT_prepare_dataset(), Bitio_Flush(), Bitio_WriteToSocket(), bitStreamEOF(), BlockComputeSNR(), blockOverrun(), BMotionSearch(), BMotionSearchNoInterp(), brainnormalize_coord(), BUCK_read_opts(), cadvise(), calc_hist(), CALC_read_opts(), Calc_Trans(), CalcDistortion(), calculate_results(), calcWithOffsets(), cfft(), cfft2d(), ChangeDirectory(), check_datum_type(), check_duplicated_short_options(), check_error(), check_for_valid_inputs(), check_func_name(), check_im_byte_order(), check_im_store_space(), check_map_func(), check_norm_dirs(), check_one_output_file(), check_outfile(), check_output_file(), check_stalled_run(), check_SUMA_surface(), check_v1hs(), check_xrestore_data(), ckalloc(), cl1_solve(), cl1_solve_res(), CL_read_opts(), cleanup(), cleanup_fork(), cleanUpAndFail(), clear_around_point(), clf(), Clp_NewParser(), clustedit3D(), cmp_chars(), cmp_doubles(), cmp_floats(), cmp_ints(), cmp_longs(), cmp_schars(), cmp_shorts(), colormap_info(), comlen(), commonprotos(), compact_results(), CompileTests(), complete_orients_str(), compress(), compressedStreamEOF(), compressOutOfMemory(), compressStream(), compute_face_vols(), compute_node_areas(), compute_node_vols(), compute_results(), ComputeBMotionLumBlock(), ComputeD0(), ComputeDiffDCTs(), ComputeFrameTable(), ComputeGOPFrames(), COND_PushCondition(), ConnectToSocket(), conv_set_ref(), convert1(), copy_surfaces(), crcError(), create_bucket(), create_gert_script(), CreateListeningSocket(), CREN_dset_axes(), CREN_render(), CREN_set_opamap(), CREN_set_viewpoint(), csfft_trigconsts(), dataline(), DC_error(), DC_fg_colortext(), DCM_CloseObject(), DCM_ImportStream(), debug_free_id(), debug_malloc_id(), debug_realloc_id(), decode_mpeg2(), def_commons(), DELAY_tsfuncV2(), delete_oldest(), demux(), detected(), dir_expansion_form(), disp_f3_point(), disp_func_t(), disp_ldp_surf_list(), disp_mri_imarr(), disp_node_list_t(), disp_numeric_data(), disp_optiondata(), disp_opts_t(), disp_param_t(), disp_parser_t(), disp_range_3dmm(), disp_range_3dmm_res(), disp_s2v_opts_t(), disp_surf_t(), disp_surf_vals(), disp_v2s_opts_t(), disp_v2s_param_t(), disp_v2s_plugin_opts(), disp_v2s_results(), dist_f3mm(), dist_fn(), DLSQ_rot_trans(), dmalloc_info(), dmalloc_report(), do_fio(), do_p1_fortran(), do_stats(), do_xrestore_stuff(), doinclude(), doReversibleTransformation(), DRAW_3D_sphere(), DRAW_fillin_CB(), DRAW_into_dataset(), DRAW_receiver(), DRAW_ttatlas_CB(), draw_xseg(), drive_MCW_grapher(), drive_MCW_imseq(), DSET2_dset_recv(), DSETN_dset_recv(), dsort(), DT_read_opts(), Dump(), dump_surf_3dt(), Dumpit(), dumpstack(), DWI_AFNI_update_graph(), DWI_NIML_create_graph(), DWI_NIML_create_newgraph(), DWI_Open_NIML_stream(), EDIT_aver_fvol(), EDIT_check_argv(), EDIT_coerce_scale_type(), EDIT_coerce_type(), EDIT_dset_items(), EDIT_filter_volume(), EDIT_main(), EDIT_one_dataset(), EDIT_substitute_brick(), EDIT_volpad(), edit_weight(), EncodeCDC(), EncodeYDC(), entrypt(), ENV_cwd(), erhand(), err(), errex(), error(), Error_Exit(), error_report(), errorExit(), estPDF_error(), evaluate_span(), evolve_bitvector_array(), EX_error(), EXP0D_worker(), exportData(), exportPixels(), exportStream(), extension_info(), extract_median(), F3D_initialize_user_data(), F77_aloc(), f__fatal(), face_load(), fail_die_malloc_die(), Fatal(), fatal_error(), fatalError(), FatalError(), FDR_error(), FFT_1dcx(), FFT_2dchirpz(), FFT_2dcx(), fft_3dec(), fft_4dec(), fft_5dec(), FFT_selection(), fill_ldp_surf_list(), fill_node_list(), fill_sopt_default(), fill_SUMA_structs(), fim3d_fimmer_compute(), FIM_error(), FIM_selection(), final_clean_up(), final_cleanup(), final_computations(), find_base_value(), find_best_span(), find_first_volume(), find_fl_file_index(), find_more_volumes(), FindBestMatch(), float_list_alloc(), Form_R_Matrix(), Frame_Init(), FramesToMPEG(), fred_CB(), Fsize_Note(), ftnstop(), FTOSH_getopts(), FTOSH_syntax(), FWHM_error(), ge4_read_header(), ge4_swap_all_bytes(), GenBFrame(), generateEPS(), GenIFrame(), GenMotionCode(), GenMPEGStream(), GenPFrame(), get_ascii_item(), get_best_shift(), get_binary_item(), get_cmask(), get_coef(), get_dfile_params(), get_dimensions(), get_fft_mag(), get_item_value(), get_line_args(), get_lsqfit(), get_mappable_surfs(), get_octant_clips(), get_options(), get_pcor(), get_pcor_thresh_coef(), get_stored_item(), get_surf_data(), get_surf_measures(), get_variance(), GetAspectRatio(), GetFrameRate(), GetRemoteDecodedRefFrame(), GetRemoteFrame(), GetUnusedFrame(), GIF_Add_To_Table(), GIF_Clear_Table(), GIF_Comment(), GIF_GCL(), GIF_Get_Code(), GIF_Get_Next_Entry(), GIF_Image_Header(), GIF_Init_Table(), GIF_Loop(), GIF_Read_File(), GIF_Screen_Header(), GIF_Send_Data(), GOPStoMPEG(), GRA_file_pixmap(), gts_surface_suma(), handle_args(), handle_tta(), HandleEvent(), hf_signal(), HI_read_opts(), hidden_NI_malloc(), hidden_NI_realloc(), HISTO_main(), huber_func(), ibeta(), Ifile_help(), image_info(), IMREG_main(), Ims_rot(), imsized_fname(), ind_printf(), init_colors(), init_extras(), init_MCW_sizes(), init_node_list(), init_options(), init_opts_t(), initialize_program(), initRateControl(), insert_list(), insert_newest(), insert_value(), iochan_fork_relay(), iochan_fork_sigfunc(), iochan_init(), iochan_recv(), iochan_send(), ioError(), IR_error(), ISQ_cropper(), ISQ_drawing_EV(), ISQ_graymap_draw(), ISQ_make_image(), ISQ_make_montage(), ISQ_manufacture_one(), ISQ_montage_CB(), ISQ_rowgraph_draw(), ISQ_saver_CB(), ISQ_set_cursor_state(), ISQ_set_image_number(), ISQ_setup_ppmto_filters(), ISQ_show_image(), ISQ_show_zoom(), ISQ_statistics_WP(), ISQ_zoom_av_CB(), JM2JPEG(), JMovie2JPEG(), JPEG_matrix_gray(), L1F_worker(), lazy_det(), license(), ListDirectory(), LSQ_worker(), main(), main_FD_EPI(), make_peel_mask(), make_plot(), make_point_list(), MAKER_4D_to_typed_fbuc(), MAKER_4D_to_typed_fim(), MAKER_4D_to_typed_fith(), malloc_track(), mangle_angle(), map_v2s_results(), matrix_file_write(), Max_func(), MB_RateOut(), MCW_build_mask(), MCW_choose_CB(), MCW_choose_integer(), MCW_choose_multi_editable_strlist(), MCW_choose_multi_strlist(), MCW_choose_ovcolor(), MCW_choose_string(), MCW_choose_timeseries(), MCW_choose_vector(), MCW_erode_clusters(), MCW_file_expand(), MCW_find_clusters(), MCW_get_intlist(), mcw_malloc_dump(), MCW_new_DC(), mem(), memplot_to_RGB_sef(), memplot_to_X11_sef(), Mhead_GenMBHeader(), Mhead_GenSequenceHeader(), mp_rle_huff_pblock(), Mpost_RLEHuffPBlock(), MREN_render(), MREN_set_graybytes(), MREN_set_min_opacity(), MREN_set_opabytes(), MREN_set_rgbbytes(), MREN_set_rgbmap(), MREN_set_rgbshorts(), MREN_set_size(), MREN_set_viewpoint(), MREN_unset_rgbmap(), MResize(), MRG_read_opts(), mri_2dalign_setup(), mri_3dalign_one(), mri_3dalign_setup(), mri_3to_rgb(), mri_aff2d_byte(), mri_aff2d_rgb(), mri_affine_bicubic(), mri_align_crao(), mri_align_dfspace(), mri_automask_image(), mri_brainormalize(), mri_complex_abs(), mri_complex_phase(), mri_delayed_lsqfit(), mri_dup2D(), mri_fft_complex(), mri_filt_fft(), mri_flippo(), mri_imcount_dicom(), mri_input_delay(), mri_lsqfit(), mri_max(), mri_maxabs(), mri_medianfilter(), mri_min(), mri_mult_to_float(), mri_multiply_complex(), mri_new_7D_generic(), mri_nsize(), mri_psinv(), mri_quantize(), mri_read(), mri_read3D_analyze75(), mri_read_1D(), mri_read_3A(), mri_read_3D(), mri_read_3D_delay(), mri_read_analyze75(), mri_read_ascii(), mri_read_dicom(), mri_read_ge4(), mri_read_many_files(), mri_read_mpeg(), mri_read_ppm3(), mri_resize(), mri_rota(), mri_rota_bilinear(), mri_rota_shear(), mri_scale_to_float(), mri_sharpen(), mri_shift2D_bilinear(), mri_short2mask(), mri_sobel(), mri_startup_lsqfit(), mri_stat_seq(), mri_swapbytes(), mri_to_byte(), mri_to_byte_scl(), mri_to_complex(), mri_to_complex_ext(), mri_to_float(), mri_to_mri(), mri_to_mri_scl(), mri_to_rgb(), mri_to_rgba(), mri_to_short(), mri_to_short_sclip(), mri_to_XImage(), mri_uncat2D(), mri_warp(), mri_warp3D_align_fitim(), mri_warp3d_align_one(), mri_warp3D_align_setup(), mri_warp3D_get_delta(), mri_watershedize(), mri_write(), mri_write_7D(), mri_write_analyze(), mri_write_angif(), mri_write_ascii(), mri_write_jpg(), mri_write_pnm(), mri_write_raw(), mri_zeropad_2D(), MTD_killfunc(), multivector_write(), my_alloc(), My_Malloc(), myMalloc(), mySignalCatcher(), mySIGSEGVorSIGBUScatcher(), nap_time_from_tr(), nc_advise(), NC_begins(), NCcoordck(), ncio_create(), ncio_new(), ncio_px_move(), NCvnrecs(), ncx_check(), new_MCW_bbox(), new_MCW_grapher(), new_PCOR_references(), new_PCOR_voxel_corr(), new_PLUGIN_interface_1999(), new_PLUGOUT_spec(), new_references(), new_riu(), new_RT_input(), new_voxel_corr(), newElementItem(), next_marker(), NI_dpr(), NI_malloc_dump(), NI_read_columns(), NI_read_element(), NI_read_URL_tmpdir(), NI_rowtype_define(), NI_stream_open(), NI_stream_reopen(), NI_stream_write(), NI_suck_stream(), NI_write_columns(), NIH_find_clusters(), NIML_to_stderr(), NLfit_error(), NLFIT_read_MODEL(), NoteFrameDone(), NotifyDecodeServerReady(), NotifyMasterDone(), NP_error(), NUD_finalize_dset_CB(), NUD_print_CB(), NUD_rotate(), old_write_ascii_item(), op_gen(), open_incoming_socket(), open_URL_hpf(), OpenBitRateFile(), output_results(), output_rms_arrays(), output_state_history(), output_ts_array(), overlapping(), p1_const(), p1_line_number(), p1put(), p1putd(), p1putdd(), p1putddd(), p1putdds(), p1putds(), p1putn(), p1puts(), pad(), parray(), parse_args(), Parse_Specifics_File(), Parse_Specifics_File_v1(), Parse_Specifics_File_v2(), parse_switches(), parset_affine(), ParseTuneParam(), path_to_dir_n_suffix(), Pbadmsg(), Pbadret(), PBAR_button_EV(), PBAR_read_bigmap(), pbm_getbit(), pbm_getc(), pbm_getint(), pbm_getrawbyte(), pbm_readmagicnumber(), pbm_readpbmrow(), pbm_writepbminit(), PC_read_opts(), PC_syntax(), PCOR_get_coef(), PCOR_get_lsqfit(), PCOR_get_mcor(), PCOR_get_pcor(), PCOR_get_pcor_and_coef(), PCOR_get_perc(), PCOR_get_variance(), PCOR_UPDATE(), PDF_write_file(), PERMTEST_compute(), Pfile(), pfit(), pgm_readpgminitrest(), pgm_readpgmrow(), pgm_writepgminit(), pgm_writepgmrowraw(), PH_fakeim(), PH_redraw(), PH_scale_CB(), pipe_color_transformer(), pixar_to_XImage(), PLOT_scatterellipse(), plotline_memplot(), PLUG_action_CB(), PLUG_get_many_plugins(), PLUG_read_plugin(), PLUG_setup_widgets(), PLUG_startup_plugin_CB(), PLUG_workprocess(), PLUGIN_init(), PLUTO_add_dset(), PLUTO_popup_worker(), PLUTO_register_timeout(), PLUTO_register_workproc(), PLUTO_remove_workproc(), PLUTO_scatterplot(), ply_describe_element(), ply_describe_other_properties(), ply_describe_property(), ply_element_count(), ply_get_element_setup(), ply_get_other_element(), ply_get_other_properties(), ply_get_property(), ply_header_complete(), ply_put_element(), ply_put_element_setup(), pm_allocarray(), pm_allocrow(), pm_closer(), pm_closew(), pm_perror(), PMotionSearch(), pnm_readpnminit(), pnm_readpnmrow(), pnm_writepnminit(), pnm_writepnmrow(), Pnotboth(), populate_nifti_image(), POWER_main(), ppm_alloccolorhash(), ppm_colorhashtocolorhist(), ppm_colorhisttocolorhash(), ppm_computecolorhash(), ppm_readppminitrest(), ppm_readppmrow(), ppm_writeppminit(), ppm_writeppmrowraw(), PPMtoYUV(), prcona(), prconi(), prconr(), PRIC_main(), print_column_headers(), print_empty_stats(), print_header(), print_plot(), print_stats_header(), print_text_marker(), print_usage(), PrintEndStats(), PrintItoIBitRate(), PrintMaxMemory(), PrintStartStats(), probe_track(), proc_finalize_shm_volumes(), proc_sigfunc(), process_args(), process_file(), process_NIML_AFNI_volumedata(), process_NIML_Node_ROI(), process_NIML_SUMA_ixyz(), Process_Options(), process_sample(), ProcessRefFrame(), project_byte_mip(), ps_arc(), ps_circle(), ps_clear(), ps_cont(), ps_epilog(), ps_label(), ps_linemod(), ps_point(), ps_prolog(), ps_rect(), ps_setfont(), ps_setrgb(), ps_setwidth(), ps_space(), ps_stroke(), Ptoken(), Put_image(), put_one_arg(), putin_fop_table(), PV2S_check_surfaces(), PV2S_disp_afni_surfaces(), PV2S_process_args(), px_double_buffer(), qh_addpoint(), qh_attachnewfacets(), qh_build_withrestart(), qh_buildhull(), qh_buildtracing(), qh_check_bestdist(), qh_check_maxout(), qh_check_point(), qh_check_points(), qh_checkconnect(), qh_checkconvex(), qh_checkfacet(), qh_checkflags(), qh_checkflipped_all(), qh_checkpolygon(), qh_checkvertex(), qh_clock(), qh_copypoints(), qh_deletevisible(), qh_determinant(), qh_detroundoff(), qh_detsimplex(), qh_detvnorm(), qh_detvridge3(), qh_distplane(), qh_errexit(), qh_errprint(), qh_facet3vertex(), qh_facetarea_simplex(), qh_facetintersect(), qh_find_newvertex(), qh_findbest(), qh_findbestfacet(), qh_findbestneighbor(), qh_findbestnew(), qh_findgood_all(), qh_findhorizon(), qh_forcedmerges(), qh_gausselim(), qh_getarea(), qh_getcenter(), qh_infiniteloop(), qh_init_qhull_command(), qh_initbuild(), qh_initflags(), qh_initialhull(), qh_initqhull_globals(), qh_initqhull_start(), qh_initstatistics(), qh_initthresholds(), qh_joggleinput(), qh_makenew_nonsimplicial(), qh_matchduplicates(), qh_matchneighbor(), qh_matchnewfacets(), qh_maxmin(), qh_maxsimplex(), qh_memalloc(), qh_memfree(), qh_meminit(), qh_meminitbuffers(), qh_memsetup(), qh_memsize(), qh_memstatistics(), qh_merge_degenredundant(), qh_mergecycle(), qh_mergecycle_all(), qh_mergecycle_ridges(), qh_mergefacet(), qh_mergevertex_neighbors(), qh_mergevertices(), qh_new_qhull(), qh_newridge(), qh_newvertex(), qh_nextfurthest(), qh_order_vertexneighbors(), qh_partitioncoplanar(), qh_point_add(), qh_postmerge(), qh_printafacet(), qh_printbegin(), qh_printcenter(), qh_printcentrum(), qh_printend(), qh_printend4geom(), qh_printextremes(), qh_printextremes_2d(), qh_printextremes_d(), qh_printfacet2geom_points(), qh_printfacet2math(), qh_printfacet3geom_points(), qh_printfacet3math(), qh_printfacet3vertex(), qh_printfacet4geom_nonsimplicial(), qh_printfacet4geom_simplicial(), qh_printfacetheader(), qh_printfacetNvertex_nonsimplicial(), qh_printfacetNvertex_simplicial(), qh_printfacetridges(), qh_printfacets(), qh_printhashtable(), qh_printhelp_degenerate(), qh_printhelp_singular(), qh_printhyperplaneintersection(), qh_printline3geom(), qh_printlists(), qh_printmatrix(), qh_printpoint3(), qh_printpointid(), qh_printpoints(), qh_printpoints_out(), qh_printridge(), qh_printspheres(), qh_printstatistics(), qh_printstatlevel(), qh_printstats(), qh_printsummary(), qh_printvdiagram(), qh_printvertex(), qh_printvertices(), qh_printvneighbors(), qh_printvnorm(), qh_printvoronoi(), qh_printvridge(), qh_produce_output(), qh_projectinput(), qh_projectpoints(), qh_qhull(), qh_readfeasible(), qh_readpoints(), qh_rename_sharedvertex(), qh_renamevertex(), qh_scalelast(), qh_scalepoints(), qh_setaddnth(), qh_setcheck(), qh_setdelnth(), qh_setdelnthsorted(), qh_setfacetplane(), qh_setfeasible(), qh_sethalfspace(), qh_sethalfspace_all(), qh_setnew_delnthsorted(), qh_setprint(), qh_setreplace(), qh_setsize(), qh_settemp(), qh_settempfree(), qh_settemppop(), qh_settemppush(), qh_settruncate(), qh_setzero(), qh_tracemerge(), qh_tracemerging(), qh_voronoi_center(), qhull_wrap(), quadrant_fimfunc(), r_add_to_boundary(), r_any_cb_apply(), r_any_cb_undo(), r_fill_resampled_data_brick(), r_gr_cb_fill(), r_gr_cb_set_range(), r_hex_str_to_long(), r_init_afni_vars(), r_init_Alg_values(), r_init_interp_vals(), r_INT_cb_fill(), r_mri_read_dicom(), r_new_resam_dset(), r_orient_str2vec(), r_wt_cb_fill(), r_wt_cb_set_range(), r_wtgr_cb_suggest_limits(), RA_error(), RAN_setup(), rcr_disp_hist(), RCREND_finalize_saveim_CB(), RCREND_reload_dataset(), RCREND_reload_func_dset(), RCREND_state_to_widgets(), rd_disp_color_info(), rd_ed(), rd_ned(), read_ascii_floats(), read_dicom_image(), read_ge_files(), read_ge_image(), read_glt_matrix(), read_input_data(), read_JPEG_file(), read_mincdim(), read_nodes_file(), read_one_time_series(), read_Pfiles(), read_quant_tables(), read_scan_script(), read_socket(), read_stdin(), read_surf_files(), read_sxyz_1D(), read_time_series(), read_URL_ftp(), read_URL_http(), read_URL_tmpdir(), ReadDecodedRefFrame(), readFile(), readFile1(), ReadFrame(), readGroupElement(), ReadInputFileNames(), ReadIOConvert(), ReadJPEG(), ReadParamFile(), readSequence(), readVRLength(), realloc_ints(), realloc_track(), realloc_vals_list(), reference_fwd_dct(), REG_command_line(), reload_DC_colordef(), REND_finalize_saveim_CB(), REND_state_to_widgets(), reset_bigcolors(), ResetFrame(), ResetPath(), resize_XImage(), robust_covar(), rotate_stdin_points(), RSF_error(), RT_3T_to_AFNI(), RT_acquire_info(), RT_check_listen(), RT_exit(), RT_fim_recurse(), RT_finish_dataset(), RT_get_3T_info(), RT_mp_comm_close(), RT_mp_comm_init(), RT_mp_comm_init_vars(), RT_mp_comm_send_data(), RT_parser_init(), RT_process_data(), RT_process_image(), RT_process_info(), RT_process_xevents(), RT_read_image(), RT_registration_2D_atend(), RT_registration_2D_onevol(), RT_registration_2D_realtime(), RT_registration_3D_atend(), RT_registration_3D_onevol(), RT_registration_3D_realtime(), RT_sigfunc(), RT_start_child(), RT_start_dataset(), RT_tell_afni_one(), RT_worker(), RWC_init_fim_colors(), RWC_read_time_series(), RWC_setup_fims(), RWC_short_overlay(), s2v_map_type(), s2v_nodes2volume(), s_1paus(), s_paus(), s_rnge(), s_stop(), safe_fork(), safe_puts(), SafeRead(), SafeWrite(), save_argtypes(), save_pgm(), save_ppm(), SC_error(), scale_up(), scan_for_angles(), scan_ge_files(), scanCompressedPixels(), sdata_from_1D(), sdata_from_default(), segment_imarr(), select_file_type(), select_transform(), send_serial(), SendDecodedFrame(), sendMTFValues(), SendRemoteFrame(), SeparateLine(), set_3dmm_bounds(), set_all_surf_vals(), set_nice_level(), set_node_list_data(), set_offset(), set_params(), set_quant_slots(), set_sample_factors(), set_smap_opts(), set_surf_results(), set_tmp_names(), set_volume_stats(), SetBrowseGlob(), SetBSearchAlg(), setdata(), SetFCodeHelper(), SetFileFormat(), SetFramePattern(), SetPixelSearch(), SetPSearchAlg(), SetReferenceFrameType(), SetupCollectQuantStats(), SetupKillDimAreas(), SetupLaplace(), SetupLocalDCT(), SetupWriteDistortions(), SFIM_getopts(), SFIM_load_intervals(), SFIM_syntax(), shear_best(), shifter(), shm_create(), SHM_nattach(), short_usage(), Show_Help(), show_maxima_s(), show_point_list_s(), show_run_stats(), ShowBBMVHistogram(), ShowBFMVHistogram(), ShowBFrameSummary(), showFileNames(), ShowIFrameSummary(), ShowPFrameSummary(), ShowPMVHistogram(), ShowRemainingTime(), SI_error(), sig_die(), simpleSort(), slist_check_user_surfs(), slist_choose_surfs(), slist_surfs_for_ldp(), Smooth_line(), SNAP_errhandler(), SNAP_make_dc(), SNAP_store_image(), sort_shortvox(), sortIt(), spearman_fimfunc(), spec2SUMA(), Specifics_Init(), SpecLookup(), sphere_voronoi_angles(), sphere_voronoi_vectors(), StartCombineServer(), StartDecodeServer(), StartIOServer(), StartMasterServer(), startproc(), startup_lsqfit(), STATS_tsfunc(), STAVG_main(), STD_colors(), store_item(), stream_info(), stree_extract_max(), studave_t2p(), studave_t2z(), suck_file(), suma2afni_surf(), SUMA_1DROI_to_DrawnROI(), SUMA_3dBRAIN_VOYAGERtoAFNI_ParseInput(), SUMA_3dCRUISEtoAFNI_ParseInput(), SUMA_3dSurfMask_ParseInput(), SUMA_add_nodes_ixyz(), SUMA_add_norms_xyz(), SUMA_add_triangles(), SUMA_AddColAtt_CompString(), SUMA_AddDsetNelCol(), SUMA_AddFillROIDatum(), SUMA_AddLink(), SUMA_AddToTailJunctionROIDatum(), SUMA_AddToTailROIDatum(), SUMA_AdvancePastNumbers(), SUMA_AFNI_Extract_Colors(), SUMA_AFNI_forward_warp_xyz(), SUMA_AfniExists(), SUMA_AfniPrefix(), SUMA_AfniView(), SUMA_Align_to_VolPar(), SUMA_Alloc_Axis(), SUMA_Alloc_CrossHair(), SUMA_Alloc_FaceSetMarker(), SUMA_Alloc_SegmentDO(), SUMA_Alloc_SphereMarker(), SUMA_Alloc_SurfaceViewer_Struct(), SUMA_Alloc_ViewState(), SUMA_Alloc_ViewState_Hist(), SUMA_Alloc_VolPar(), SUMA_allocate2D(), SUMA_allocate_FaceSet_Edge_Neighb(), SUMA_Allocate_SPI(), SUMA_AllocateDrawnROI(), SUMA_AllocateROI(), SUMA_append_replace_string(), SUMA_AppendToROIdatum(), SUMA_Apply_VolReg_Trans(), SUMA_ApplyAffine(), SUMA_AreaDiff(), SUMA_AssembleAllROIList(), SUMA_AssembleColorPlaneList(), SUMA_assignColors(), SUMA_AssignTriBranch(), SUMA_ATF_change_value(), SUMA_ATF_SetValue(), SUMA_AxisText(), SUMA_BestStandardView(), SUMA_BinarySuck(), SUMA_BinaryZeroSearch(), SUMA_binSearch(), SUMA_BrainVoyager_Read(), SUMA_BrainVoyager_Read_vmr(), SUMA_BreakInodeLink(), SUMA_BrushStrokeToNodeStroke(), SUMA_Build_Cluster_From_Node(), SUMA_Build_Cluster_From_Node_NoRec(), SUMA_Build_FirstNeighb(), SUMA_Build_Mask_AllROI(), SUMA_BuildMenu(), SUMA_ButtClose_pushed(), SUMA_ButtOpen_pushed(), SUMA_CalcNeighbDist(), SUMA_CalculateNodeAreas(), SUMA_cb_AfniLink_toggled(), SUMA_cb_CloseDrawROIWindow(), SUMA_cb_closeSumaCont(), SUMA_cb_closeSurfaceCont(), SUMA_cb_CloseSwitchCmap(), SUMA_cb_CloseSwitchColPlane(), SUMA_cb_CloseSwitchGroup(), SUMA_cb_CloseSwitchROI(), SUMA_cb_closeViewerCont(), SUMA_cb_Cmap_Load(), SUMA_cb_ColPlane_Delete(), SUMA_cb_ColPlane_Load(), SUMA_cb_createSumaCont(), SUMA_cb_createSurfaceCont(), SUMA_cb_createViewerCont(), SUMA_cb_doneSumaCont(), SUMA_cb_DrawROI_Delete(), SUMA_cb_DrawROI_Finish(), SUMA_cb_DrawROI_Join(), SUMA_cb_DrawROI_Load(), SUMA_cb_DrawROI_Redo(), SUMA_cb_DrawROI_Save(), SUMA_cb_DrawROI_Undo(), SUMA_cb_Dset_Load(), SUMA_cb_FileClose(), SUMA_cb_FileLoadView(), SUMA_cb_FileOpenSpec(), SUMA_cb_FileOpenSurf(), SUMA_cb_FileSaveView(), SUMA_cb_helpMessageLog(), SUMA_cb_helpUsage(), SUMA_cb_moreSumaInfo(), SUMA_cb_moreSurfInfo(), SUMA_cb_moreViewerInfo(), SUMA_cb_newSumaCont(), SUMA_cb_search_text(), SUMA_cb_SelectSwitchCmap(), SUMA_cb_SelectSwitchColPlane(), SUMA_cb_SelectSwitchGroup(), SUMA_cb_SelectSwitchROI(), SUMA_cb_set_threshold(), SUMA_cb_SetCmapMode(), SUMA_cb_SetCoordBias(), SUMA_cb_SetDrawROI_SaveMode(), SUMA_cb_SetDrawROI_SaveWhat(), SUMA_cb_SetDrawROI_WhatDist(), SUMA_cb_SetRenderMode(), SUMA_cb_SwitchBrightness(), SUMA_cb_SwitchCmap(), SUMA_cb_SwitchIntensity(), SUMA_cb_SwitchThreshold(), SUMA_cb_toggle_crosshair(), SUMA_cb_toggle_node_in_focus(), SUMA_cb_toggle_selected_faceset(), SUMA_cb_viewSumaCont(), SUMA_cb_viewSurfaceCont(), SUMA_cb_viewViewerCont(), SUMA_cb_XHalock_toggled(), SUMA_cb_XHaviewlock_toggled(), SUMA_cb_XHlock_toggled(), SUMA_cb_XHviewlock_toggled(), SUMA_CheckOnSpecFile(), SUMA_Chung_Smooth_Weights(), SUMA_ClusterCenterofMass(), SUMA_Cmap_To_SO(), SUMA_Cmap_To_SO_old(), SUMA_cmap_wid_display(), SUMA_cmap_wid_graphicsInit(), SUMA_cmap_wid_handleRedisplay(), SUMA_cmap_wid_input(), SUMA_coarsen_ParseInput(), SUMA_ColPlane_NewDimFact(), SUMA_ColPlane_NewOpacity(), SUMA_ColPlane_NewOrder(), SUMA_ColType2TypeCast(), SUMA_ConvexHullSurface(), SUMA_Convexity_Engine(), SUMA_coord_file(), SUMA_Create_1dData(), SUMA_Create_ColorScaledVect(), SUMA_Create_CommonFields(), SUMA_create_empty_surface(), SUMA_Create_MemTrace(), SUMA_Create_MorphInfo(), SUMA_Create_SO_map(), SUMA_CreateActionStack(), SUMA_createColGradient(), SUMA_CreateDrawROIWindow(), SUMA_CreateDsetPointer(), SUMA_CreateFileSelectionDialogStruct(), SUMA_CreateIcosahedron(), SUMA_CreateInode(), SUMA_CreateInodeLink(), SUMA_CreateList(), SUMA_CreateLock_rbg(), SUMA_CreateMessageList(), SUMA_CreateOverlayPointer(), SUMA_CreateScrolledList(), SUMA_CreateSumaContStruct(), SUMA_CreateTable(), SUMA_CreateTextShell(), SUMA_CreateTextShellStruct(), SUMA_DeleteROI(), SUMA_DestroyList(), SUMA_Dijkstra(), SUMA_disp_dmat(), SUMA_disp_dvect(), SUMA_disp_mat(), SUMA_disp_vecdmat(), SUMA_disp_vecmat(), SUMA_disp_vect(), SUMA_disp_vecucmat(), SUMA_display(), SUMA_divEdge(), SUMA_dPercRange(), SUMA_dPoint_At_Distance(), SUMA_dqsortrow(), SUMA_Draw_SO_ROI(), SUMA_DrawAxis(), SUMA_DrawLineAxis(), SUMA_DrawMesh(), SUMA_DrawROI_NewLabel(), SUMA_DrawROI_NewValue(), SUMA_DrawSegmentDO(), SUMA_DrawWindowLine(), SUMA_EmptyColorList(), SUMA_Engine(), SUMA_EquateSurfaceAreas(), SUMA_EquateSurfaceSize(), SUMA_EquateSurfaceVolumes(), SUMA_existDO(), SUMA_existSO(), SUMA_expose(), SUMA_Extension(), SUMA_FakeIt(), SUMA_Fetch_OverlayPointer(), SUMA_FillColorList(), SUMA_FillDsetNelCol(), SUMA_FillNelCol(), SUMA_FillToMask(), SUMA_FillToVoxelMask(), SUMA_Find_IminImax(), SUMA_Find_OpenDX_Object_Class(), SUMA_Find_OpenDX_Object_Name(), SUMA_FindClusters(), SUMA_FindNgrAttributeElement(), SUMA_findSO_inDOv(), SUMA_FindVoxelsInSurface(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_FinishedROI(), SUMA_flip_orient(), SUMA_FormAfnidset(), SUMA_FormatMessage(), SUMA_FormNeighbOffset(), SUMA_FormSOListToSendToAFNI(), SUMA_fqsortrow(), SUMA_free2D(), SUMA_Free_Displayable_Object(), SUMA_Free_IsInBox(), SUMA_Free_IsInSphere(), SUMA_Free_Surface_Object(), SUMA_Free_SurfaceViewer_Struct(), SUMA_FreeActionStackData(), SUMA_FreeEngineData(), SUMA_FreeEngineListData(), SUMA_FreeMessageListData(), SUMA_FreeOverlayPointer(), SUMA_FreeROIDatum(), SUMA_FreeSurfer_Read_eng(), SUMA_FreeSurfer_ReadBin_eng(), SUMA_FreeSurfer_WritePatch(), SUMA_FromIntEdgeToIntEdge(), SUMA_FromToRotation(), SUMA_FS_Write(), SUMA_generateEPS(), SUMA_Get_AFNI_Default_Color_Maps(), SUMA_Get_isosurface_datasets(), SUMA_Get_NodeIncident(), SUMA_GetAreaDiffRange(), SUMA_GetColorList(), SUMA_GetContour(), SUMA_GetDO_Type(), SUMA_GetEyeAxis(), SUMA_GetLargestBackroundOrder(), SUMA_GetM2M_NN(), SUMA_GetNextCommand(), SUMA_getoffsets(), SUMA_getPatch(), SUMA_GetSelectionLine(), SUMA_GetSmallestForegroundOrder(), SUMA_GetStandardMap(), SUMA_graphicsInit(), SUMA_handleRedisplay(), SUMA_help_message(), SUMA_HighlightBox(), SUMA_Householder(), SUMA_Init_SurfCont_CrossHair(), SUMA_Init_SurfCont_SurfParam(), SUMA_InitializeDrawROIWindow(), SUMA_InitializeEngineListData(), SUMA_inNodeNeighb(), SUMA_input(), SUMA_Interpret_AFNIColor(), SUMA_IntersectionStrip(), SUMA_IO_args_2_spec(), SUMA_iRGB_to_OverlayPointer(), SUMA_isConsistent(), SUMA_isdROIrelated(), SUMA_isInodeLink(), SUMA_isinpoly(), SUMA_isNumString(), SUMA_isSelfIntersect(), SUMA_ixyzsort_surface(), SUMA_JumpFocusFace(), SUMA_JumpFocusNode(), SUMA_JumpIndex(), SUMA_JumpXYZ(), SUMA_leave_EV(), SUMA_leave_TableField(), SUMA_Linearize_Color_Map(), SUMA_LinkToPointer(), SUMA_Load_Spec_Surf(), SUMA_Load_Surface_Object_eng(), SUMA_Load_Surface_Object_Wrapper(), SUMA_LoadCmapFile(), SUMA_LoadColorPlaneFile(), SUMA_LoadDsetFile(), SUMA_LoadNimlDset(), SUMA_LoadPrepInVol(), SUMA_LoadSegDO(), SUMA_LoadSpec_eng(), SUMA_LoadVisualState(), SUMA_LookAtCoordinates(), SUMA_Make_Edge_List_eng(), SUMA_make_vnlist(), SUMA_MakeColorMap(), SUMA_MakeColorMap_v2(), SUMA_MakeConsistent(), SUMA_makeNI_CrossHair(), SUMA_makeNI_SurfIJK(), SUMA_makeNI_SurfINORM(), SUMA_makeNI_SurfIXYZ(), SUMA_MapRefRelative(), SUMA_mapStateChanged(), SUMA_MapSurface(), SUMA_MarchingCubesSurface(), SUMA_Mark_Tri(), SUMA_MarkLineSurfaceIntersect(), SUMA_MaskDsetByClustList(), SUMA_MemberFaceSets(), SUMA_Mesh_Area(), SUMA_Mesh_IJK2Mesh_IJK_nel(), SUMA_Mesh_Volume(), SUMA_MixColors(), SUMA_MixOverlays(), SUMA_momentum(), SUMA_morphToStd(), SUMA_MT_intersect_triangle(), SUMA_nel_stdout(), SUMA_New_ViewState(), SUMA_NewDsetPointer(), SUMA_NewGeometryInViewer(), SUMA_NextState(), SUMA_niml_call(), SUMA_niml_hangup(), SUMA_niml_workproc(), SUMA_NIMLDrawnROI_to_DrawnROI(), SUMA_nimlSO2SO(), SUMA_NodeInput(), SUMA_NodePath_to_EdgePath(), SUMA_NodePath_to_TriPath_Inters(), SUMA_NodePath_to_TriPath_Inters_OLD(), SUMA_NodeVal2irgba_nel(), SUMA_NodeXYZ2NodeXYZ_nel(), SUMA_oDsetNel2nDsetNgr(), SUMA_Offset_GeomSmooth(), SUMA_OpenDrawnROI(), SUMA_OpenDrawnROI_1D(), SUMA_OpenDrawnROI_NIML(), SUMA_OpenDrawROIWindow(), SUMA_OpenDx_Object_Data(), SUMA_OpenDx_Object_Header_Field(), SUMA_OpenDX_Read(), SUMA_OpenDX_Read_CruiseVolHead(), SUMA_OpenGLStateReset(), SUMA_orcode_to_orstring(), SUMA_OrientTriangles(), SUMA_orstring_to_orcode(), SUMA_Overlays_2_GLCOLAR4(), SUMA_pad_str(), SUMA_pad_string(), SUMA_Paint_SO_ROIplanes(), SUMA_ParseInput_basics(), SUMA_ParseLHS_RHS(), SUMA_Patch2Surf(), SUMA_Pattie_Volume(), SUMA_PercRange(), SUMA_Plane_Equation(), SUMA_Ply_Read(), SUMA_Ply_Write(), SUMA_Point_At_Distance(), SUMA_Point_To_Line_Distance(), SUMA_Point_To_Point_Distance(), SUMA_PolySurf3(), SUMA_PopUpMessage(), SUMA_PositionWindowRelative(), SUMA_postRedisplay(), SUMA_Prefix2SurfaceName(), SUMA_PrepAddmappableSO(), SUMA_PrependToROIdatum(), SUMA_PrepSO_GeomProp_GL(), SUMA_PrevState(), SUMA_Print_PlaneOrder(), SUMA_Print_Surface_Object(), SUMA_process_environ(), SUMA_process_NIML_data(), SUMA_ProcessBrushStroke(), SUMA_PROGRAM_NAME_ParseInput(), SUMA_ProjectSurfaceToSphere(), SUMA_PromptApply_cb(), SUMA_qhull_wrap(), SUMA_RangeTableCell_EV(), SUMA_read1D(), SUMA_Read_2Ddfile(), SUMA_Read_2Dfile(), SUMA_Read_dfile(), SUMA_Read_file(), SUMA_Read_IRGB_file(), SUMA_read_ppm(), SUMA_Read_SpecFile(), SUMA_Read_SureFit_Param(), SUMA_ReadCharStdin(), SUMA_readColor(), SUMA_readFSannot(), SUMA_readFScurv(), SUMA_ReadNumStdin(), SUMA_ReadSegDO(), SUMA_RedisplayAllShowing(), SUMA_RefreshDsetList(), SUMA_register_workproc(), SUMA_RegisterCommand(), SUMA_RegisterDO(), SUMA_RegisterEngineData(), SUMA_RegisterEngineListCommand(), SUMA_RegisterMessage(), SUMA_RegisterSpecSO(), SUMA_ReleaseActionStackData(), SUMA_ReleaseEngineData(), SUMA_ReleaseEngineListElement(), SUMA_ReleaseLink(), SUMA_ReleaseMessageListElement(), SUMA_ReleaseOverlay(), SUMA_remove_workproc(), SUMA_remove_workproc2(), SUMA_RemoveDO(), SUMA_RenderToPixMap(), SUMA_ReportDrawnROIDatumLength(), SUMA_Reposition_Touchup(), SUMA_resize(), SUMA_response(), SUMA_ROIv2dataset(), SUMA_ROIv2Grpdataset(), SUMA_SampBias_ParseInput(), SUMA_Save_Surface_Object(), SUMA_SaveSOascii(), SUMA_SaveVisualState(), SUMA_ScaleToMap(), SUMA_ScaleToMap_alaAFNI(), SUMA_ScaleToMapOptInit(), SUMA_SendToAfni(), SUMA_SendToSuma(), SUMA_set_cmap_options(), SUMA_SetAllRemixFlag(), SUMA_SetCmapMenuChoice(), SUMA_SetcSV(), SUMA_SetLight0(), SUMA_SetLocalRemixFlag(), SUMA_SetNumForeSmoothing(), SUMA_SetRangeTableTit_EV(), SUMA_SetRangeValue(), SUMA_SetRemixFlag(), SUMA_SetScaleRange(), SUMA_SetScaleThr(), SUMA_SetSVForegroundColor(), SUMA_SetupSVforDOs(), SUMA_Show_ColorOverlayPlanes(), SUMA_Show_CommonFields(), SUMA_Show_DOv(), SUMA_Show_Edge_List(), SUMA_Show_FreeSurfer(), SUMA_Show_FS_ColorTable(), SUMA_Show_IO_args(), SUMA_Show_MT_intersect_triangle(), SUMA_Show_NI_str_ar(), SUMA_Show_OpenDX_Struct(), SUMA_Show_SO_map(), SUMA_Show_SPI(), SUMA_show_STB(), SUMA_Show_SureFit(), SUMA_Show_SurfaceViewer_Struct(), SUMA_Show_SurfClust_list(), SUMA_Show_ViewState(), SUMA_Show_VolPar(), SUMA_ShowAllVisuals(), SUMA_ShowBrushStroke(), SUMA_ShowDrawnROI(), SUMA_ShowDrawnROIDatum(), SUMA_ShowDset(), SUMA_ShowList(), SUMA_ShowMemTrace(), SUMA_ShowMeSome(), SUMA_ShowMeTheChildren(), SUMA_ShowNel(), SUMA_ShowPatch(), SUMA_ShowScaleToMapOpt(), SUMA_ShowSpecStruct(), SUMA_ShowVisual(), SUMA_sigfunc(), SUMA_SmoothAttr_Neighb(), SUMA_SortedAxisSegmentList(), SUMA_SOVolPar2VolPar_nel(), SUMA_spec_select_surfs(), SUMA_spec_set_map_refs(), SUMA_SphereQuality(), SUMA_StretchToFitLeCerveau(), SUMA_StringAppend(), SUMA_StringAppend_va(), SUMA_StringToNum(), SUMA_Suggest_Touchup(), SUMA_Suggest_Touchup_Grad(), SUMA_SureFit_Read_Coord(), SUMA_SureFit_Read_Topo(), SUMA_SureFit_Write(), SUMA_Surf_Plane_Intersect(), SUMA_Surf_Plane_Intersect_ROI(), SUMA_Surface_Curvature(), SUMA_SurfaceFileName(), SUMA_SurfaceMetrics_eng(), SUMA_SurfClust_list_2_DsetMask(), SUMA_SurfGridIntersect(), SUMA_SurfNorm(), SUMA_SurfToSurf_ParseInput(), SUMA_swap_spec_entries(), SUMA_SwitchGroups(), SUMA_SwitchSO(), SUMA_SwitchState(), SUMA_TableF_cb_label_change(), SUMA_Take_A_Hike(), SUMA_Taubin_Smooth(), SUMA_Taubin_Smooth_TransferFunc(), SUMA_tesselate(), SUMA_THD_3dmm_to_dicomm(), SUMA_THD_dicomm_to_3dmm(), SUMA_ThreshVal2ScalePos(), SUMA_triangulateRow(), SUMA_TriInput(), SUMA_TriSurf3v(), SUMA_truncate_string(), SUMA_unique_name_ind(), SUMA_UniqueInt(), SUMA_UniqueInt_ind(), SUMA_UnlinkFromPointer(), SUMA_UnRegisterDO(), SUMA_UpdateNodeValField(), SUMA_UpdateViewerTitle(), SUMA_UpdateViewerTitle_old(), SUMA_UpdateXhairField(), SUMA_VEC_Read(), SUMA_VEC_Write(), SUMA_Version(), SUMA_VolDiff(), SUMA_VolPar_Attr(), SUMA_VolParFromDset(), SUMA_VolSurf_help(), SUMA_WhatAreYouToMe(), SUMA_whichDO(), SUMA_WhichState(), SUMA_WhichSV(), SUMA_whichTri(), SUMA_workprocess(), SUMA_World2ScreenCoords(), SUMA_write1D(), SUMA_Write_DrawnROI_1D(), SUMA_Write_DrawnROI_NIML(), SUMA_writeColorFile(), SUMA_writeFSfile(), SUMA_writeSpecFile(), SUMA_X_SurfaceViewer_Create(), SUMA_XhairInput(), SUMA_XYZ_XYZmap(), SUMA_XYZmap_XYZ(), SUMA_z_doubqsort(), SUMA_z_dqsort(), SUMA_z_dqsort_nsc(), SUMA_z_qsort(), SumaToGts(), surf_ave_radius(), surf_to_node_list(), surf_triangle_match(), swap_strings(), sxyz_1D_to_nlist(), SYM_expand_ranges(), Syntax(), T3D_check_outliers(), T3D_initialize_user_data(), T3D_open_view_CB(), T3D_orient_av_CB(), T3D_origin_av_CB(), T3D_poperr(), T3D_read_images(), T3D_save_file_CB(), T3D_size_av_CB(), T3D_type_av_CB(), t_getn_float_double(), t_getn_float_long(), TAG_write_CB(), targetRateControl(), TCAT_read_opts(), tcp_accept(), terminate(), testdims(), testf(), testStream(), TFIM_getopts(), TFIM_syntax(), THD_3dim_from_block(), THD_alloc_datablock(), THD_autonudge(), THD_check_idcodes(), THD_copy_dset_subs(), THD_copy_file(), THD_datablock_from_atr(), THD_delete_datablock(), THD_extract_float_brick(), THD_fetch_1D(), THD_fetch_dataset(), THD_fetch_many_datasets(), THD_generic_detrend(), THD_get_many_timeseries(), THD_init_session(), THD_load_1D(), THD_load_3D(), THD_load_analyze(), THD_load_ctfmri(), THD_load_ctfsam(), THD_load_datablock(), THD_load_minc(), THD_load_mpeg(), THD_load_nifti(), THD_mask_clust(), THD_mask_erode(), THD_mask_fillin_once(), thd_mask_from_brick(), THD_matrix_to_orientation(), THD_normalize_flist(), THD_open_1D(), THD_open_3D(), THD_open_3dcalc(), THD_open_analyze(), THD_open_dataset(), THD_open_minc(), THD_open_nifti(), THD_open_tcat(), THD_read_dvecmat(), THD_rename_dataset_files(), THD_rota3D(), THD_rota3D_matvec(), THD_rota_vol(), THD_rota_vol_2byte(), THD_rota_vol_byte(), THD_rota_vol_matvec(), THD_rota_vol_matvec_2byte(), THD_rowfillin_short(), THD_warp3D(), THD_write_1D(), THD_write_3dim_dataset(), THD_write_atr(), THD_write_datablock(), THD_write_minc(), THD_write_nifti(), THD_zeropad(), The_Help(), TheEnd1(), trealloc(), trimunder(), tross_Add_Note(), ts_fprint(), ts_loop(), TS_parse_tpattern(), TS_syntax(), ts_to_ftime(), ts_write(), TT_read_opts(), TT_syntax(), TT_whereami(), TTRR_save_CB(), Tune_Init(), UC_read_opts(), UC_syntax(), UN_error(), uncompress(), uncompressOutOfMemory(), uncompressStream(), UnQuantZig(), unusuality(), update_PCOR_references(), update_references(), update_voxel_corr(), UpdatePath(), updateRateControl(), updateVBVBuffer(), Usage(), usage(), UTL_VerifyCreatePath(), v2s_adjust_endpts(), v2s_apply_filter(), v2s_map_type(), v2s_write_outfile_1D(), v2s_write_outfile_niml(), valid_resam_inputs(), validate_datasets(), validate_option_lists(), validate_options(), validate_surface(), validate_v2s_inputs(), vector_write(), verify_node_list(), verify_parser_expr(), verify_surf_t(), vertex_load(), vexit(), VL_command_line(), vol2surf(), VOLREG_main(), volume_match(), volume_search(), VPBug(), vstep_print(), w_ed(), w_ned(), WA_error(), wait_for_socket(), WaitForDecodedFrame(), WaitForOutputFile(), wanted(), warn(), warning(), weighted_index(), WINsorize(), write_3dtime(), write_afni_data(), write_afni_fict(), write_afni_fizt(), write_ascii_item(), write_binary_item(), write_bucket_data(), write_data_to_file(), write_float(), write_indent(), write_JPEG_file(), write_many_ts(), write_one_ts(), write_output(), write_results(), write_scalar_type(), write_stdout(), write_table(), write_ts_array(), write_ud(), WriteDecodedFrame(), writets(), wrong_widget(), x_rsne(), xdr_check(), xhairs_to_image_pts(), XImage_to_mri(), XSAVE_input(), XSAVE_output(), xxx_get_colormap(), yuv2rgb_c_init(), yyparse(), and ZCAT_read_opts(). |
| Frame_N = input('\nWhich column corresponds to regressor coefficient? (1, 2, 3, ...) ') |
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| means defined in AFNI doc README attributes Opt Frames = 1 |
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| GroupAna m Bethesda MD Define the function name for easy referencing FuncName = 'GroupAna.m' |
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| end For the last chunk of which are not a whole set Not an elegant i = Z |
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| end Read in each file For each there should have Info |
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| Throw out those four which do not exist for intensity = zeros(D1, D2, D3, N_Brik) |
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Referenced by add_dataset_list_to_PLUGIN_interface(), add_dataset_to_PLUGIN_interface(), add_number_to_PLUGIN_interface(), add_option_to_PLUGIN_interface(), add_overlaycolor_to_PLUGIN_interface(), add_string_to_PLUGIN_interface(), add_timeseries_to_PLUGIN_interface(), AFNI_choose_dataset_CB(), AFNI_plugin_button(), AFNI_process_setup(), basis_write_iresp(), basis_write_sresp(), calculate_results(), DC_add_overlay_color(), DC_Err(), DC_find_overlay_color(), DC_Fit(), DC_IRF(), DRAW_choose_CB(), DRAW_undo_butlab(), get_inputs(), glutAddMenuEntry(), glutAddSubMenu(), glutChangeToMenuEntry(), glutChangeToSubMenu(), GRA_setshift_action_CB(), ISQ_disp_act_CB(), ISQ_montage_action_CB(), L1F_detrend(), L1F_fitter(), L1F_worker(), LSQ_detrend(), LSQ_fitter(), LSQ_worker(), main(), MCW_action_area(), MCW_choose_editable_strlist(), MCW_choose_integer(), MCW_choose_multi_editable_strlist(), MCW_choose_multi_strlist(), MCW_choose_string(), MCW_choose_strlist(), MCW_choose_timeseries(), MCW_choose_vector(), new_MCW_arrowval(), new_MCW_colormenu(), new_MCW_optmenu(), new_PLUGIN_interface(), new_PLUGIN_interface_1999(), NL_error(), NL_fitter(), NL_worker(), nlfit(), NOTES_choose_CB(), NUD_3string(), NUD_choose_CB(), NUD_threestring(), output_ts_array(), parray(), PLUG_choose_dataset_CB(), PLUTO_popup_dset_chooser(), PV2S_disp_afni_surfaces(), r_gr_mk_main_frame(), r_wt_mk_main_frame(), RCREND_choose_CB(), readPreamble(), REND_choose_CB(), report_results(), setMenuItem(), SUMA_AFNI_Extract_Colors(), SUMA_AllocateDrawnROI(), SUMA_AllocateROI(), SUMA_BuildMenu(), SUMA_cb_createSurfaceCont(), SUMA_cb_createViewerCont(), SUMA_CreateArrowField(), SUMA_CreateTextField(), SUMA_FreeMenuVector(), TSGEN_main(), TTRR_setup_widgets(), v2s_write_outfile_1D(), WA_err(), WA_fit(), WA_fwt(), WA_sgnl(), write_3dtime(), write_afni_data(), write_bucket_data(), and write_ts_array(). |
| Should it be changed to a different name instead of FL ntot = 1 |
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Definition at line 300 of file GroupAna.m.
Referenced by AIVVV_imseq_getim(), AIVVV_imseq_popup(), chfit(), iochan_force_clear(), iochan_recvall(), iochan_send(), iochan_sendall(), ISQ_record_getim(), ISQ_record_open(), ISQ_record_update(), ISQ_statistics_WP(), main(), mcw_load(), mri_1D_fromstring(), mri_warp3D_get_delta(), NI_set_dimen(), NI_stream_fillbuf(), NI_write_columns(), NI_write_element(), PLUTO_imseq_addto(), PLUTO_imseq_getim(), PLUTO_imseq_popup(), quotize_string_vector(), RCREND_imseq_getim(), RCREND_open_imseq(), RCREND_update_imseq(), REND_imseq_getim(), REND_open_imseq(), REND_update_imseq(), SHM_sendall(), SNAP_imseq_getim(), SUMA_input(), and THD_mask_clip_neighbors(). |
| end For the last chunk of which are not a whole set of |
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Definition at line 1561 of file GroupAna.m.
Referenced by calculate_acontrasts(), calculate_adifferences(), calculate_ameans(), calculate_bcontrasts(), calculate_bdifferences(), calculate_bmeans(), calculate_xdifferences(), calculate_xmeans(), check_for_valid_inputs(), def_commons(), initialize(), and main(). |
| flip before subscripting Doing flip because I want vary the levels starting the last factor in stead of the first scpt = fliplr(file(i).v) |
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| end end Voxel independent stuff[err, Qd, s, termname, nterms, sindices, dfbothSS, modw, modwo, tnames, dfterm, dfe, Contr] = PreProc(ntot, NF, group, varnames, FL, Contr, cov, unbalanced) |
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| end end For each there should have FL (2).N_level*FL(3).N_level subbriks % X( For each subbrik |
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Referenced by AREN_set_size(), ART_send_control_info(), DRAW_ttatlas_CB(), dup_NC_attrarrayV(), dup_NC_dimarrayV(), dup_NC_vararrayV(), estimate_gfw(), extract_index(), extract_xyz(), ISQ_plot_label(), main(), MREN_set_size(), ncx_len_NC_attr(), ncx_len_NC_dim(), ncx_len_NC_string(), ncx_len_NC_var(), new_NC_string(), new_x_NC_attr(), new_x_NC_var(), output_results(), plot_strip_init(), plot_ts_init(), plot_ts_mem(), SUMA_Mesh_Volume(), THD_3dim_dataset_to_brick(), THD_autonudge(), VPLoadScale(), vpScale(), wrt_L(), xdr_check(), and xdr_encode(). |
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Definition at line 1524 of file GroupAna.m.
Referenced by basym(), idct_col(), idct_row(), signal_model(), SUMA_FindVoxelsInSurface(), SUMA_FindVoxelsInSurface_SLOW(), SUMA_isinbox(), SUMA_isinsphere(), VPCompAC00G(), VPCompAC11B(), VPCompAC1NB(), VPCompAC1NS(), VPCompAC1PB(), VPCompAC31B(), VPCompAC32B(), VPCompAC3NB(), VPCompAC3NS(), VPCompAC3PB(), VPCompAR00G(), VPCompAR11B(), VPCompAR1NB(), VPCompAR1NS(), VPCompAR1PB(), VPCompAR31B(), VPCompAR32B(), VPCompAR3NB(), VPCompAR3NS(), VPCompAR3PB(), VPRenderAffine(), and vpShadeTable(). |
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Definition at line 2067 of file GroupAna.m.
Referenced by __glutMenuItemEnterOrLeave(), AFNI_brick_to_mri(), AIVVV_imseq_getim(), arg_verify(), c_type_decl(), call0(), call1(), call2(), call3(), call4(), callk(), chkgot(), commlen(), ComputeBMotionBlock(), consbinop(), conspower(), data_value(), dataline(), do_init_data(), do_lio(), do_p1_const(), do_p1_expr(), do_p1_list(), docommon(), dodecahedron(), doentry(), doughnut(), drawBox(), EDIT_dset_items(), entrypt(), fixexttype(), Frame_New(), get_ascii_item(), get_binary_item(), get_callvalue_from_PLUGIN_interface(), get_fmt(), get_item_value(), get_stored_item(), impldcl(), inferdcl(), Inline(), ioset(), ISQ_but_disp_CB(), ISQ_record_getim(), ISQ_redisplay(), l_read(), l_write(), Len(), lengtype(), list_arg_types(), list_decls(), make_one_const(), mkarg(), mktmp(), mktmp0(), mktmpn(), mpeg2_header_picture(), mtype_size(), nc_cktype(), nc_def_var(), nc_put_att(), nc_put_att_double(), nc_put_att_float(), nc_put_att_int(), nc_put_att_long(), nc_put_att_schar(), nc_put_att_short(), nc_put_att_uchar(), nctypelen(), ncx_howmany(), ncx_len_NC_attrV(), ncx_pad_getn_Idouble(), ncx_pad_getn_Ifloat(), ncx_pad_getn_Iint(), ncx_pad_getn_Ilong(), ncx_pad_getn_Ischar(), ncx_pad_getn_Ishort(), ncx_pad_getn_Iuchar(), ncx_pad_putn_Idouble(), ncx_pad_putn_Ifloat(), ncx_pad_putn_Iint(), ncx_pad_putn_Ilong(), ncx_pad_putn_Ischar(), ncx_pad_putn_Ishort(), ncx_pad_putn_Iuchar(), ncx_szof(), new_MCW_textwin(), new_MCW_textwin_2001(), new_NC_attr(), new_NC_var(), new_x_NC_attr(), nextarg(), old_write_ascii_item(), out_call(), out_const(), p1_const(), p1get_const(), p1put(), p1putd(), p1putdd(), p1putddd(), p1putdds(), p1putds(), p1putn(), p1puts(), pad_common(), PLUGIN_imseq_getim(), PLUTO_imseq_getim(), pr_att_vals(), process_as_floats(), process_data(), protowrite(), put_one_arg(), putcall(), putconst(), putentries(), putio(), putmnmx(), putpower(), qh_clearcenters(), qh_initstatistics(), qh_newstats(), qh_nostatistic(), qh_printstatlevel(), RCREND_imseq_getim(), readref(), REND_imseq_getim(), ResetFrame(), save_argtypes(), setdata(), setimpl(), SetReferenceFrameType(), settype(), SNAP_imseq_getim(), SPLASH_imseq_getim(), stfcall(), store_item(), SUMA_CreateArrowField(), SUMA_CreateTable(), SUMA_writeSpecFile(), T3D_getim(), teapot(), THD_3dim_from_block(), thd_mask_from_brick(), type_name(), updateRateControl(), v1h_get_NC_attr(), v1h_get_NC_attrarray(), v1h_get_NC_dimarray(), v1h_get_nc_type(), v1h_get_NC_vararray(), v1h_get_NCtype(), v1h_put_NCtype(), vpWindow(), wr_array_init(), wr_one_init(), wr_output_values(), wr_struct(), write_ascii_item(), write_assigned_fmts(), write_binary_item(), write_char_init(), write_namelists(), x_rsne(), and x_wsne(). |
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