diff --git a/melodic.cc b/melodic.cc index 25386ab6c086875ec7648d25e253533ea3f1db40..d991c0e426c1e816efa9fbe4d60523ceb05a36f6 100644 --- a/melodic.cc +++ b/melodic.cc @@ -123,7 +123,7 @@ int main(int argc, char *argv[]){ } if(!leaveloop){ if(opts.paradigmfname.value().length()>0) - opts.pca_dim.set_T(std::max(opts.pca_dim.value(),melodat.get_param().Ncols()+3*opts.retrystep-1); + opts.pca_dim.set_T(std::max(opts.pca_dim.value(),melodat.get_param().Ncols()+3*opts.retrystep-1)); message(endl << "Restarting MELODIC using -d " << opts.pca_dim.value() << endl << endl); diff --git a/meloptions.h b/meloptions.h index a5044f2b80f21359f7bb7ad080af5619ef31d9dd..ba86f82b60cb954aacc02ad2684d96980a46d15b 100644 --- a/meloptions.h +++ b/meloptions.h @@ -111,6 +111,7 @@ class MelodicOptions { Option<string> guessfname; Option<string> paradigmfname; + Option<string> axials_str; Option<int> dummy; Option<int> repeats; @@ -337,6 +338,9 @@ class MelodicOptions { paradigmfname(string("--init_pca"), string(""), string("file name of FEAT paradigm file (design.mat) for PCA initialisation"), false, requires_argument, false), + axials_str(string("--report_maps"), string(" -s 2 -A 950 "), + string("control string for spatial map images (see slicer)"), + false, requires_argument), dummy(string("--dummy"), 0, string("number of dummy volumes"), false, requires_argument,false), @@ -437,6 +441,7 @@ class MelodicOptions { options.add(guessfname); options.add(paradigmfname); + options.add(axials_str); options.add(dummy); options.add(repeats); options.add(nlconst1); diff --git a/melreport.cc b/melreport.cc index 6110a1965dcfee46348bc8d63c5bd50eb8e8ad66..ba8c1b2032ccb2766f9c03b8178de98ed2d34bcb 100644 --- a/melreport.cc +++ b/melreport.cc @@ -92,8 +92,7 @@ namespace Melodic{ //save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"), // melodat.tempInfo); sprintf(instr," "); - strcat(instr," -s 2"); - strcat(instr," -A 950 "); + strcat(instr,axials_instr.c_str()); strcat(instr,string(report.appendDir(mmodel.get_prefix()+ "_thresh.png")).c_str()); newpic.set_title(string("Component No. "+num2str(cnum)+ @@ -390,8 +389,7 @@ namespace Melodic{ //save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"), // melodat.tempInfo); sprintf(instr," "); - strcat(instr," -s 2"); - strcat(instr," -A 950 "); + strcat(instr,axials_instr.c_str()); strcat(instr,string(report.appendDir(mmodel.get_prefix()+"_thresh"+ num2str(tctr)+".png")).c_str()); newpic.set_title(string("Component No. "+num2str(cnum)+ @@ -487,8 +485,7 @@ namespace Melodic{ //save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"), // melodat.tempInfo); sprintf(instr," "); - strcat(instr," -s 2"); - strcat(instr," -A 950 "); + strcat(instr,axials_instr.c_str()); strcat(instr,string(report.appendDir(mmodel.get_prefix()+ ".png")).c_str()); newpic.set_title(string("Component No. "+num2str(cnum)+ @@ -522,8 +519,8 @@ namespace Melodic{ char instr[10000]; sprintf(instr," "); - strcat(instr,"-l render1 -s 2"); - strcat(instr," -A 950 "); + strcat(instr,"-l render1 "); + strcat(instr,axials_instr.c_str()); strcat(instr,string(report.appendDir(mmodel.get_prefix()+ "_prob.png")).c_str()); newpic.set_title(string("Component No. "+num2str(cnum)+ @@ -660,8 +657,7 @@ namespace Melodic{ //save_volume(newvol,report.appendDir(prefix+"rendered"), // melodat.tempInfo); sprintf(instr," "); - strcat(instr," -s 2"); - strcat(instr," -A 950 "); + strcat(instr,axials_instr.c_str()); strcat(instr,string(report.appendDir(prefix+ ".png")).c_str()); newpic.set_title(string("Component No. "+num2str(cnum)+ diff --git a/melreport.h b/melreport.h index 115ea78883fa849374fc854e4e675279921af0f7..be2b5edd26d601e5297b3f791fe4c6ee400e2a6e 100644 --- a/melreport.h +++ b/melreport.h @@ -90,6 +90,7 @@ namespace Melodic{ navigator << "<A HREF=\"log.html\" target=\"_top\">Log</A> - "; navigator <<"Components: "; navigator.flush(); + axials_instr = opts.axials_str.value(); } } @@ -301,7 +302,8 @@ namespace Melodic{ Log IChtml; Log IChtml2; - + string axials_instr; + void IC_rep_det(MelGMix &mmodel, int cnum, int dim); string int2str(int n){