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unit prefs;
{$H+}
interface
uses
inifiles, define_types,SysUtils,classes,turbolesion,dialogsx;
function DoLesion (var lPrefs: TLDMPrefs): boolean;
procedure SetDefaultPrefs (var lPrefs: TLDMPrefs);
function WarnIfLowNCrit(lnSubj,lnCrit: integer): boolean;
//procedure ReadParamStr;
implementation
uses nifti_img, hdr,nifti_hdr, valformat,StatThdsUtil,filename, unpm;
procedure SetDefaultPrefs (var lPrefs: TLDMPrefs);
begin
lPrefs.tTest := true;
lPrefs.BMtest := false;
lPrefs.Ltest := false;
lPrefs.nPermute := 0;
lPrefs.CritPct := -1;//use default in val file
lPrefs.ExplicitMaskName := '';
lPrefs.ValFilename := '';
lPrefs.Outname := '';
end;
function noVariance (lRA: singlep; lnSubj: integer): boolean;
var
lI : integer;
begin
result := false;
if lnSubj < 2 then exit;
for lI := 2 to lnSubj do
if lRA^[1] <> lRA^[lI] then
exit;
result := true;
end;
function WarnIfLowNCrit(lnSubj,lnCrit: integer): boolean;
//returns true if warning generated
begin
result := (round(lnSubj * 0.15) ) > lnCrit; //15%
if result then
Showmsg('Warning: low statistical power as tests computed for voxels damaged in at least '+inttostr(lnCrit) +' people. Solution: change Design value "Ignore voxels damaged in less than N%".');
end;
function DoLesion (var lPrefs: TLDMPrefs): boolean;
label
666;
var
lFact,lnFactors,lSubj,lnSubj,lnSubjAll,lMaskVoxels,lnCritV,lCritPctV: integer;
lImageNames,lImageNamesAll: TStrings;
lPredictorList: TStringList;
lTemp4D,lMaskname,lFactname: string;
lMaskHdr: TMRIcroHdr;
lMultiSymptomRA,lSymptomRA: singleP;
begin
if (not lPrefs.BMtest) and (not lPrefs.ttest) and (not lPrefs.LTest) then begin
NPMmsg('Error: you need to compute at least on test [options/test menu]');
exit;
end;
lImageNamesAll:= TStringList.Create; //not sure why TStrings.Create does not work???
lImageNames:= TStringList.Create; //not sure why TStrings.Create does not work???
if not GetValCore(lPrefs.ValFilename, lnSubjAll,lnFactors,lMultiSymptomRA,lImageNamesAll,lnCritV,lCritPctV,lPredictorList) then begin
NPMmsg('Error with VAL file');
goto 666;
end;
if lPrefs.critPct < 0 then //-1 denotes using the values specified in the VAL file
lPrefs.critPct := lCritPctV;
lTemp4D := CreateDecompressed4D(lImageNamesAll);
if (lnSubjAll < 1) or (lnFactors < 1) then begin
NPMmsg('Not enough subjects ('+inttostr(lnSubjAll)+') or factors ('+inttostr(lnFactors)+').');
goto 666;
end;
WarnIfLowNCrit(lnSubjAll, round( (lnSubjAll*lPrefs.CritPct)/100));
lMaskname := lImageNamesAll[0];
if not NIFTIhdr_LoadHdr(lMaskname,lMaskHdr) then begin
NPMmsg('Error reading 1st mask.');
goto 666;
end;
lMaskVoxels := ComputeImageDataBytes8bpp(lMaskHdr);
if (lMaskVoxels < 2) or (not CheckVoxels(lMaskname,lMaskVoxels,0)){make sure there is uncompressed .img file} then begin
NPMmsg('Mask file size too small.');
goto 666;
end;
if (lPrefs.OutName = '') or (not DirExists(extractfiledir(lPrefs.Outname))) then begin
lPrefs.Outname := extractfiledir(lPrefs.ValFilename)+pathdelim+'results.nii.gz';
NPMmsg('Output stored as '+lPrefs.Outname);
end;
for lFact := 1 to lnFactors do begin
NPMMsgClear;
NPMMsg(GetKVers);
lImageNames.clear;
for lSubj := 1 to lnSubjAll do
if (not lPrefs.LTest) or (lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)] = 0) OR (lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)] = 1) THEN begin
{$IFNDEF FPC}if lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)] <> NaN then {$ENDIF}
lImageNames.Add(lImageNamesAll[lSubj-1]);
end else begin
NPMMsg('Data rejected: behavior must be zero or one for binomial test '+lImageNamesAll.Strings[lSubj-1]);
end;
lnSubj := lImageNames.Count;
if lnSubj > 2 then begin
getmem(lSymptomRA,lnSubj * sizeof(single));
lnSubj := 0;
for lSubj := 1 to lnSubjAll do begin
if (not lPrefs.LTest) or (lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)] = 0) OR (lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)] = 1) THEN begin
{$IFNDEF FPC}if lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)] <> NaN then begin
{$ELSE} begin{$ENDIF}
inc(lnSubj);
lSymptomRA^[lnSubj] := lMultiSymptomRA^[lSubj+((lFact-1)*lnSubjAll)];
end; //valid value
end; //not binomial, or 1/0
end; //for each subject
NPMMsg('Threads: '+inttostr(gnCPUThreads));
lFactName := lPredictorList.Strings[lFact-1];
lFactName := LegitFilename(lFactName,lFact);
NPMMsg('Factor = '+lFactname);
For lSubj := 1 to lnSubj do
NPMMsg (lImageNames.Strings[lSubj-1] + ' = '+realtostr(lSymptomRA^[lSubj],2) );
NPMMsg('Total voxels = '+inttostr(lMaskVoxels));
lPrefs.nCrit := round( (lnSubj*lPrefs.CritPct)/100);
NPMMsg('Only testing voxels damaged in at least '+inttostr(lPrefs.nCrit)+' individual[s]');
NPMMsg('Number of Lesion maps = '+inttostr(lnSubj));
if not CheckVoxelsGroupX(lImageNames,lMaskHdr {lMaskVoxels}) then begin
NPMMsg('Error: File dimensions differ from mask.');
goto 666;
end;
if noVariance (lSymptomRA,lnSubj) then
NPMMsg('Error no variability in behavioral data ')
else
TurboLDM (lImageNames, lMaskHdr, lPrefs, lSymptomRA, lFactname,lPrefs.OutName);
Freemem(lSymptomRA);
end else begin
NPMMsg('At least 2 individuals required to compute statistics for '+lPredictorList.Strings[lFact-1]);
end; //lnsubj > 2
end; //for each factor
if lnSubjAll > 0 then begin
Freemem(lMultiSymptomRA);
end;
666:
lImageNames.Free;
lImageNamesAll.Free;
lPredictorList.Free;
DeleteDecompressed4D(lTemp4D);
end;
(*procedure ShowHelp;
begin
NPMMsg('usage ''npm [options] -o resultsfilname valfilename'' ');
NPMMsg(' Options ');
NPMMsg(' -c: critical percent 0..100 ');
NPMMsg(' -p: permutations 0..4000 ');
NPMMsg(' -t: Test [1=Liebermeister, 2=TTest, 4=BMtest, 6=t&BMtests');
NPMMsg(' -o: Output filename');
NPMMsg('examples:');
NPMMsg(' npm -c 25 -p 1000 -o c:\results.nii.gz c:\mri\data.val');
NPMMsg(' npm -c 25 -o "c:\program files\results.hdr" c:\mri\data.val');
end;
procedure ReadParamStr;
var
lStr: String;
I,lError: integer;
lCommandChar: Char;
lSingle: single;
lHelpShown: boolean;
lPrefs: TLDMPrefs;
begin
if (ParamCount < 1) then exit;
SetDefaultPrefs(lPrefs);
lHelpShown := false;
lStr := paramstr(0);
lStr := extractfilename(lStr);
lStr := string(StrUpper(PChar(lStr))) ;
if (ParamCount > 0) then begin
I := 0;
repeat
lStr := '';
repeat
inc(I);
if I = 1 then
lStr := ParamStr(I)
else begin
if lStr <> '' then
lStr := lStr +' '+ ParamStr(I)
else
lStr := ParamStr(I);
end;
if (length(lStr)>1) and (lStr[1] = '-') and (ParamCount > I) then begin //special command
//-z= zoom, -f= format [png,jpeg,bmp], -o= output directory
lCommandChar := UpCase(lStr[2]);
inc(I);
lStr := ParamStr(I);
lStr := string(StrUpper(PChar(lStr))) ;
case lCommandChar of
'C','P','T': begin //CritPct
Val(lStr,lSingle,lError);
if lError = 0 then begin
if lCommandChar = 'C' then
lPrefs.CritPct := round(lSingle)
else if lCOmmandChar = 'P' then
lPrefs.nPermute := round(lSingle)
else if lCOmmandChar = 'T' then begin
case round(lSingle) of
1: begin lPrefs.LTest := true; lPrefs.Ttest := false; lPrefs.BMtest := false; end;
2: begin lPrefs.LTest := false; lPrefs.Ttest := true; lPrefs.BMtest := false; end;
4: begin lPrefs.LTest := false; lPrefs.Ttest := false; lPrefs.BMtest := true; end;
6: begin lPrefs.LTest := false; lPrefs.Ttest := true; lPrefs.BMtest := true; end;
//1=Liebermeister, 2=TTest, 4=BMtest, 6=t&BMtests
end;//xxx
end;
end; //not lError
end; //C= CritPct,P=permutations,T=test
'O': begin //output filename
lPrefs.OutName :=lStr;
end;
end; //case lStr[2]
lStr := '';
end; //special command
until (I=ParamCount) or (fileexists(lStr)) {or (gAbort)};
if fileexists(lStr) then begin
//lStr := GetLongFileName(lStr);
lPrefs.ValFilename := lStr;
//if lPrefs.OutName = '' then
// lPrefs.Outname := extractfiledir(paramstr(0))+pathdelim+'results.nii.gz';
NPMMsg ('output ' + lPrefs.Outname);
NPMMsg ('val file: '+lPrefs.ValFilename);
DoLesion(lPrefs);
//MainForm.close;
end else begin
NPMMsg('Error: unable to find '+lStr);
if not lHelpShown then
Showhelp;
lHelpShown := true;
end;
until I >= ParamCount;
end else begin
ShowHelp;
end;{param count > 0}
end; *)
end.
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