00001 function [err, out_fn] = Norm (InBrik, N_runs, run, run_norm, run_mask, foutid_log)
00002 %
00003 % [err, norm_fn] = Norm(InBrik, N_runs, run)
00004 %
00005 %Purpose:
00006 %
00007 % Normalize the original dataset so that the beta values in 3dDeconvolve would be automatically percent signal change.
00008 %
00009 %Input Parameters:
00010 %
00011 %
00012 %
00013 %Output Parameters:
00014 % err : 0 No Problem
00015 % : 1 Problems
00016 %
00017 %
00018 %
00019 %Key Terms:
00020 %
00021 %More Info :
00022 %
00023 %
00024 %
00025 %
00026 % Author : Gang Chen
00027 % Date : Mon Oct 20 11:26:38 EDT 2003
00028 % SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
00029
00030
00031 %Define the function name for easy referencing
00032 FuncName = 'Norm';
00033
00034 %Debug Flag
00035 DBG = 1;
00036
00037 %initailize return variables
00038 err = 1;
00039
00040 [InBrikPrefix, InBrikView, InBrikExt] = AfniPrefix (InBrik);
00041 rm_cmmd = 'rm -f ';
00042
00043 %Originally 3dClipLevel was used to generate a cliplevel for each run,
00044 %then a step function chops off those voxel outside of the brain.
00045 %But due to the concern of losing the sensitive amygdala and orbitofrontal cortex,
00046 %it might be better to run 3dAutomask, which is roughly equivalent to
00047 %3dClipLevel but would protect amygdala and orbitofrontal cortex regions
00048 %from being masked.
00049
00050 %create command for executing 3dAutomask
00051 if (run_mask.do == 1),
00052 automask_fn = sprintf('%s_msk', InBrikPrefix);
00053 automask = sprintf('3dAutomask -dilate %i -prefix %s %s%s', run_mask.N_dilate, automask_fn, InBrikPrefix, InBrikView);
00054 fprintf(2, '\nRunning: %s\n', automask);
00055 fprintf(foutid_log, '%s\n', automask);
00056 [s,w] = system(automask);
00057 if (s),
00058 fprintf(2,'Error during 3dAutomask: \n\n%s\n\n',w);
00059 while (1); fprintf(2,'Halted: Ctrl+c to exit'); pause; end
00060 end
00061 rm_cmmd = sprintf('%s %s%s%s', rm_cmmd, automask_fn, InBrikView, InBrikExt);
00062
00063 %If no normalization, do masking
00064 if (run_norm == 0),
00065 out_fn = sprintf('%s_mask', InBrikPrefix);
00066 mask_signal = sprintf('3dcalc -fscale -a %s%s \\\n', InBrikPrefix, InBrikView);
00067 mask_signal = sprintf('%s -b %s%s \\\n', mask_signal, automask_fn, InBrikView);
00068 mask_signal = sprintf('%s -expr "a*b" \\\n', mask_signal);
00069 mask_signal = sprintf('%s -prefix %s', mask_signal, out_fn);
00070 fprintf(2, '\nRunning: %s\n', mask_signal);
00071 fprintf(foutid_log, '%s\n', mask_signal);
00072 [s,w] = system(mask_signal);
00073 if (s),
00074 fprintf(2,'Error during 3dcalc: \n\n%s\n\n',w);
00075 while (1); fprintf(2,'Halted: Ctrl+c to exit'); pause; end
00076 end
00077 end
00078 rm_cmmd = sprintf('%s %s%s%s', rm_cmmd, automask_fn, InBrikView, InBrikExt);
00079 end
00080
00081 if (run_norm == 1), %for normalization
00082 out_fn = sprintf('%s_norm', InBrikPrefix);
00083 concat = sprintf('3dTcat -prefix %s ', out_fn);
00084
00085 for (i=1:1:N_runs),
00086
00087 %store each mean dataset in a temporary file, and delete it before leaving this function.
00088 mean_fn = sprintf('%s_mean%i', InBrikPrefix, i);
00089 get_mean = sprintf('3dTstat -mean -prefix %s %s%s''[%i..%i]''', mean_fn, InBrikPrefix, InBrikView, run(i).first, run(i).last);
00090 fprintf(2, '\nRunning: %s\n', get_mean);
00091 fprintf(foutid_log, '%s\n', get_mean);
00092 [s, w] = system(get_mean);
00093 if (s),
00094 fprintf(2,'Error at running 3dTstat: \n\n\n%s\n', w);
00095 while (1); fprintf(2,'Halted: Ctrl+c to exit');pause; end
00096 end
00097
00098 %normalizing
00099 % norm_signal = sprintf('3dcalc -datum float -a %s%s''[%i..%i]'' \\\n', InBrikPrefix, InBrikView, run(i).first, run(i).last);
00100 norm_signal = sprintf('3dcalc -fscale -a %s%s''[%i..%i]'' \\\n', InBrikPrefix, InBrikView, run(i).first, run(i).last);
00101 norm_signal = sprintf('%s -b %s%s \\\n', norm_signal, mean_fn, InBrikView);
00102 if (run_mask.do == 1),
00103 norm_signal = sprintf('%s -c %s%s \\\n', norm_signal, automask_fn,InBrikView);
00104 % norm_signal = sprintf('%s -expr "(a/b*100)*step(b-clip_level)" \\\n', norm_signal);
00105 norm_signal = sprintf('%s -expr "(a/b*100)*c" \\\n', norm_signal);
00106 else norm_signal = sprintf('%s -expr "a/b*100" \\\n', norm_signal);
00107 end
00108 norm_out_fn = sprintf('%s_norm%i', InBrikPrefix, i);
00109 norm_signal = sprintf('%s -prefix %s', norm_signal, norm_out_fn);
00110 fprintf(2, '\nRunning: %s\n', norm_signal);
00111 fprintf(foutid_log, '%s\n', norm_signal);
00112 [s,w] = system(norm_signal);
00113 if (s),
00114 fprintf(2,'Error during 3dcalc: \n\n%s\n\n',w);
00115 while (1); fprintf(2,'Halted: Ctrl+c to exit'); pause; end
00116 end
00117
00118 %Concatenate the above files together
00119 concat = sprintf('%s %s%s%s', concat, norm_out_fn, InBrikView, InBrikExt);
00120
00121 %create remove command for deleting those individual percent signal change and mean file for each run.
00122 rm_cmmd = sprintf('%s %s%s%s %s%s%s', rm_cmmd, norm_out_fn, InBrikView, InBrikExt, mean_fn, InBrikView, InBrikExt);
00123
00124 end
00125
00126 %Concatenate all runs back together
00127 fprintf(2, '\nRunning: %s\n', concat);
00128 fprintf(foutid_log, '%s\n', concat);
00129 [s,w] = system(concat);
00130 if (s),
00131 fprintf(2,'Error during running 3dTcat: \n\n%s\n\n',w);
00132 while (1); fprintf(2,'Halted: Ctrl+c to exit'); pause; end
00133 end
00134 end
00135
00136 %Don't forget to remove those temporary files above.
00137 fprintf(2, '\nRemoving: %s\n', rm_cmmd);
00138 fprintf(foutid_log, '%s\n', rm_cmmd);
00139 [s,w] = system(rm_cmmd);
00140 if (s),
00141 fprintf(2,'Error during rm: \n\n%s\n\n',w);
00142 while (1); fprintf(2,'Halted: Ctrl+c to exit'); pause; end
00143 end
00144
00145 err = 0;
00146 return;
