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write_fsf

PURPOSE ^

write_fsf(fsf);

SYNOPSIS ^

function write_fsf(fsf)

DESCRIPTION ^

 write_fsf(fsf);

 Writes a FEAT structure file (.fsf) for use with FSL's FEAT analysis package

 fsf is structure with all of the parameters necessary to write out the .fsf
 file. The default field values are set in create_fsf.m

 NOTE: This is still a work in progress. 
 Fortunately, the FEAT GUI will read a partially completed setup file.  
 In effect, it should be possible to create a template for any given analysis
 and then fill a few fields with pointers to the subject specific files.

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function write_fsf(fsf)
0002 % write_fsf(fsf);
0003 %
0004 % Writes a FEAT structure file (.fsf) for use with FSL's FEAT analysis package
0005 %
0006 % fsf is structure with all of the parameters necessary to write out the .fsf
0007 % file. The default field values are set in create_fsf.m
0008 %
0009 % NOTE: This is still a work in progress.
0010 % Fortunately, the FEAT GUI will read a partially completed setup file.
0011 % In effect, it should be possible to create a template for any given analysis
0012 % and then fill a few fields with pointers to the subject specific files.
0013 
0014 % 04/22/05 Petr Janata
0015 % 09/05/05 PJ - completed first functional version
0016 
0017 % Open the .fsf file based on information in the structure
0018 
0019 fid = fopen(fullfile(fsf.fsldir,'design.fsf'),'wt');
0020 
0021 fsf_str = sprintf([ ...
0022       '\n# FEAT version number' ...
0023       '\nset fmri(version) %1.2f\n'], fsf.version);
0024 fprintf(fid,'%s', fsf_str);
0025 
0026 fsf_str = sprintf([ ...
0027       '\n# Are we in MELODIC?' ...
0028       '\nset fmri(inmelodic) 0\n']);
0029 fprintf(fid,'%s',fsf_str);
0030 
0031 fsf_str = sprintf([...
0032       '\n# Analysis level' ...
0033       '\n# 1 : First-level analysis' ...
0034       '\n# 2 : Higher-level analysis' ...
0035       '\nset fmri(level) %d\n'], fsf.level);
0036 fprintf(fid,'%s', fsf_str);
0037 
0038 fsf_str = sprintf([...
0039       '\n# Which stages to run' ...
0040       '\n# 0 : No first-level analysis (registration and/or group stats only)' ...
0041       '\n# 7 : Full first-level analysis' ...
0042       '\n# 1 : Pre-Stats' ...
0043       '\n# 3 : Pre-Stats + Stats' ...
0044       '\n# 2 :             Stats' ...
0045       '\n# 6 :             Stats + Contrasts, Thresholding, Rendering' ...
0046       '\n# 4 :                     Contrasts, Thresholding, Rendering' ...
0047       '\nset fmri(analysis) %d\n'], fsf.analysis);
0048 fprintf(fid,'%s', fsf_str);
0049 
0050 if fsf.version == 5.4
0051   fsf_str = sprintf([...
0052         '\n# Delay before starting (hours)' ...
0053         '\nset fmri(delay) %d\n'], fsf.delay);
0054   fprintf(fid,'%s', fsf_str);
0055 end
0056 
0057 fsf_str = sprintf([...
0058       '\n# Use relative filenames' ...
0059       '\nset fmri(relative_yn) %d\n'], fsf.relative_yn);
0060 fprintf(fid,'%s', fsf_str);
0061 
0062 fsf_str = sprintf([...
0063       '\n# Balloon help' ...
0064       '\nset fmri(help_yn) %d\n'], fsf.help_yn);
0065 fprintf(fid,'%s', fsf_str);
0066 
0067 fsf_str = sprintf([...
0068       '\n# Run Featwatcher' ...
0069       '\nset fmri(featwatcher_yn) %d\n'], fsf.featwatcher_yn);
0070 fprintf(fid,'%s', fsf_str);
0071 
0072 fsf_str = sprintf([...
0073       '\n# Cleanup first-level standard-space images' ...
0074       '\nset fmri(sscleanup_yn) %d\n'], fsf.sscleanup_yn);
0075 fprintf(fid,'%s', fsf_str);
0076 
0077 fsf_str = sprintf([...
0078       '\n# Output directory' ...
0079       '\nset fmri(outputdir) "%s"\n'], fsf.outputdir);
0080 fprintf(fid,'%s', fsf_str);
0081 
0082 fsf_str = sprintf([...
0083       '\n# TR(s)' ...
0084       '\nset fmri(tr) %1.2f\n'], fsf.tr);
0085 fprintf(fid,'%s', fsf_str);
0086 
0087 fsf_str = sprintf([...
0088       '\n# Total volumes' ...
0089       '\nset fmri(npts) %d\n'], fsf.npts);
0090 fprintf(fid,'%s', fsf_str);
0091 
0092 fsf_str = sprintf([...
0093       '\n# Delete volumes' ...
0094       '\nset fmri(ndelete) %d\n'], fsf.ndelete);
0095 fprintf(fid,'%s', fsf_str);
0096 
0097 if fsf.version == 5.98
0098   fsf_str = sprintf([...
0099       '\n# Perfusion tag/control order' ...
0100       '\nset fmri(tagfirst) %d\n'], fsf.tagfirst);
0101   fprintf(fid,'%s', fsf_str);
0102 end
0103   
0104 fsf_str = sprintf([...
0105       '\n# Number of first-level analyses' ...
0106       '\nset fmri(multiple) %d\n'], fsf.multiple);
0107 fprintf(fid,'%s', fsf_str);
0108 
0109 fsf_str = sprintf([...
0110       '\n# Higher-level input type' ...
0111       '\n# 1 : Inputs are lower-level FEAT directories' ...
0112       '\n# 2 : Inputs are cope images from FEAT directories' ...
0113       '\nset fmri(inputtype) %d\n'], fsf.inputtype);
0114 fprintf(fid,'%s', fsf_str);
0115 
0116 fsf_str = sprintf([...
0117       '\n# Carry out pre-stats processing?' ...
0118       '\nset fmri(filtering_yn) %d\n'], fsf.filtering_yn);
0119 fprintf(fid,'%s', fsf_str);
0120 
0121 fsf_str = sprintf([...
0122       '\n# Brain/background threshold, %%' ...
0123       '\nset fmri(brain_thresh) %d\n'], fsf.brain_thresh);
0124 fprintf(fid,'%s', fsf_str);
0125 
0126 if fsf.version == 5.98
0127   fsf_str = sprintf([...
0128       '\n# Critical z for design efficiency calculation' ...
0129       '\nset fmri(critical_z) %1.2f\n'], fsf.critical_z);
0130   fprintf(fid,'%s', fsf_str);
0131 
0132   fsf_str = sprintf([...
0133       '\n# Noise level' ...
0134       '\nset fmri(noise) %1.6f\n'], fsf.noise);
0135   fprintf(fid,'%s', fsf_str);
0136 
0137   fsf_str = sprintf([...
0138       '\n# Noise AR(1)' ...
0139       '\nset fmri(noisear) %1.6f\n'], fsf.noisear);
0140   fprintf(fid,'%s', fsf_str);
0141 end
0142   
0143 fsf_str = sprintf([...
0144       '\n# Post-stats-only directory copying' ...
0145       '\n# 0 : Overwrite original post-stats results' ...
0146       '\n# 1 : Copy original FEAT directory for new Contrasts, Thresholding, Rendering' ...
0147       '\nset fmri(newdir_yn) %d\n'], fsf.newdir_yn);
0148 fprintf(fid,'%s', fsf_str);
0149 
0150 fsf_str = sprintf([...
0151       '\n# Slice timing correction' ...
0152       '\n# 0 : None' ...
0153       '\n# 1 : Regular up (0, 1, 2, 3, ...)' ...
0154       '\n# 2 : Regular down' ...
0155       '\n# 3 : Use slice order file' ...
0156       '\n# 4 : Use slice timings file' ...
0157       '\n# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )' ...
0158       '\nset fmri(st) %d\n'], fsf.st);
0159 fprintf(fid,'%s', fsf_str);
0160 
0161 fsf_str = sprintf([...
0162       '\n# Slice timings file' ...
0163       '\nset fmri(st_file) "%s"\n'], fsf.st_file);
0164 fprintf(fid,'%s', fsf_str);
0165 
0166 fsf_str = sprintf([...
0167       '\n# Motion correction' ...
0168       '\n# 0 : None' ...
0169       '\n# 1 : MCFLIRT' ...
0170       '\nset fmri(mc) %d\n'], fsf.mc);
0171 fprintf(fid,'%s', fsf_str);
0172 
0173 fsf_str = sprintf([...
0174       '\n# Spin-history (currently obsolete)' ...
0175       '\nset fmri(sh_yn) %d\n'], fsf.sh_yn);
0176 fprintf(fid,'%s', fsf_str);
0177 
0178 fsf_str = sprintf([...
0179       '\n# BET brain extraction' ...
0180       '\nset fmri(bet_yn) %d\n'], fsf.bet_yn);
0181 fprintf(fid,'%s', fsf_str);
0182 
0183 fsf_str = sprintf([...
0184       '\n# Spatial smoothing FWHM (mm)' ...
0185       '\nset fmri(smooth) %d\n'], fsf.smooth);
0186 fprintf(fid,'%s', fsf_str);
0187 
0188 fsf_str = sprintf([...
0189       '\n# Intensity normalization' ...
0190       '\nset fmri(norm_yn) %d\n'], fsf.norm_yn);
0191 fprintf(fid,'%s', fsf_str);
0192 
0193 if fsf.version == 5.98
0194   fsf_str = sprintf([...
0195       '\n# Perfusion subtraction' ...
0196       '\nset fmri(perfsub_yn) %d\n'], fsf.perfsub_yn);
0197   fprintf(fid,'%s', fsf_str);
0198 end
0199 
0200 fsf_str = sprintf([...
0201       '\n# Highpass temporal filtering' ...
0202       '\nset fmri(temphp_yn) %d\n'], fsf.temphp_yn);
0203 fprintf(fid,'%s', fsf_str);
0204 
0205 fsf_str = sprintf([...
0206       '\n# Lowpass temporal filtering' ...
0207       '\nset fmri(templp_yn) %d\n'], fsf.templp_yn);
0208 fprintf(fid,'%s', fsf_str);
0209 
0210 fsf_str = sprintf([...
0211       '\n# MELODIC ICA data exploration' ...
0212       '\nset fmri(melodic_yn) %d\n'], fsf.melodic_yn);
0213 fprintf(fid,'%s', fsf_str);
0214 
0215 fsf_str = sprintf([...
0216       '\n# Carry out main stats?' ...
0217       '\nset fmri(stats_yn) %d\n'], fsf.stats_yn);
0218 fprintf(fid,'%s', fsf_str);
0219 
0220 fsf_str = sprintf([...
0221       '\n# Carry out prewhitening?' ...
0222       '\nset fmri(prewhiten_yn) %d\n'], fsf.prewhiten_yn);
0223 fprintf(fid,'%s', fsf_str);
0224 
0225 if fsf.version == 5.98
0226   fsf_str = sprintf([...
0227       '\n# Add motion parameters to model' ...
0228       '\n# 0 : No' ...
0229       '\n# 1 : Yes' ...
0230       '\nset fmri(motionevs) %d\n'], fsf.motionevs);
0231   fprintf(fid,'%s', fsf_str);
0232 
0233   fsf_str = sprintf([...
0234       '\n# Robust outlier detection in FLAME?' ...
0235       '\nset fmri(robust_yn) %d\n'], fsf.robust_yn);
0236   fprintf(fid,'%s', fsf_str);
0237 end
0238 
0239 fsf_str = sprintf([...
0240       '\n# Higher-level modelling' ...
0241       '\n# 3 : Fixed effects' ...
0242       '\n# 0 : Mixed Effects: Simple OLS' ...
0243       '\n# 2 : Mixed Effects: FLAME (stage 1 only)' ...
0244       '\n# 1 : Mixed Effects: FLAME (full)' ...
0245       '\nset fmri(mixed_yn) %d\n'], fsf.mixed_yn);
0246 fprintf(fid,'%s', fsf_str);
0247 
0248 fsf_str = sprintf([...
0249       '\n# Number of EVs' ...
0250       '\nset fmri(evs_orig) %d' ...
0251       '\nset fmri(evs_real) %d\n'], fsf.evs_orig,fsf.evs_real);
0252 fprintf(fid,'%s', fsf_str);
0253 
0254 if fsf.version == 5.98
0255   fsf_str = sprintf('set fmri(evs_vox) %d\n', fsf.evs_vox);
0256   fprintf(fid,'%s', fsf_str);
0257 end
0258 
0259 fsf_str = sprintf([...
0260       '\n# Number of contrasts' ...
0261       '\nset fmri(ncon_orig) %d' ...
0262       '\nset fmri(ncon_real) %d\n'], fsf.ncon_orig, fsf.ncon_real);
0263 fprintf(fid,'%s', fsf_str);
0264 
0265 fsf_str = sprintf([...
0266       '\n# Number of F-tests' ...
0267       '\nset fmri(nftests_orig) %d' ...
0268       '\nset fmri(nftests_real) %d\n'], fsf.nftests_orig, fsf.nftests_real);
0269 fprintf(fid,'%s', fsf_str);
0270 
0271 fsf_str = sprintf([...
0272       '\n# Add constant column to design matrix? (obsolete)' ...
0273       '\nset fmri(constcol) %d\n'], fsf.constcol);
0274 fprintf(fid,'%s', fsf_str);
0275 
0276 fsf_str = sprintf([...
0277       '\n# Carry out post-stats steps?' ...
0278       '\nset fmri(poststats_yn) %d\n'], fsf.poststats_yn);
0279 fprintf(fid,'%s', fsf_str);
0280 
0281 fsf_str = sprintf([...
0282       '\n# Pre-threshold masking?' ...
0283       '\nset fmri(threshmask) "%s"\n'], fsf.threshmask);
0284 fprintf(fid,'%s', fsf_str);
0285 
0286 fsf_str = sprintf([...
0287       '\n# Thresholding' ...
0288       '\n# 0 : None' ...
0289       '\n# 1 : Uncorrected' ...
0290       '\n# 2 : Voxel' ...
0291       '\n# 3 : Cluster' ...
0292       '\nset fmri(thresh) %d\n'], fsf.thresh);
0293 fprintf(fid,'%s', fsf_str);
0294 
0295 fsf_str = sprintf([...
0296       '\n# P threshold' ...
0297       '\nset fmri(prob_thresh) %1.4f\n'], fsf.prob_thresh);
0298 fprintf(fid,'%s', fsf_str);
0299 
0300 fsf_str = sprintf([...
0301       '\n# Z threshold' ...
0302       '\nset fmri(z_thresh) %1.2f\n'], fsf.z_thresh);
0303 fprintf(fid,'%s', fsf_str);
0304 
0305 fsf_str = sprintf([...
0306       '\n# Z min/max for colour rendering' ...
0307       '\n# 0 : Use actual Z min/max' ...
0308       '\n# 1 : Use preset Z min/max' ...
0309       '\nset fmri(zdisplay) %d\n'], fsf.zdisplay);
0310 fprintf(fid,'%s', fsf_str);
0311 
0312 fsf_str = sprintf([...
0313       '\n# Z min in colour rendering' ...
0314       '\nset fmri(zmin) %d\n'], fsf.zmin);
0315 fprintf(fid,'%s', fsf_str);
0316 
0317 fsf_str = sprintf([...
0318       '\n# Z max in colour rendering' ...
0319       '\nset fmri(zmax) %d\n'], fsf.zmax);
0320 fprintf(fid,'%s', fsf_str);
0321 
0322 fsf_str = sprintf([...
0323       '\n# Colour rendering type' ...
0324       '\n# 0 : Solid blobs' ...
0325       '\n# 1 : Transparent blobs' ...
0326       '\nset fmri(rendertype) %d\n'], fsf.rendertype);
0327 fprintf(fid,'%s', fsf_str);
0328 
0329 fsf_str = sprintf([...
0330       '\n# Background image for higher-level stats overlays' ...
0331       '\n# 1 : Mean highres' ...
0332       '\n# 2 : First highres' ...
0333       '\n# 3 : Mean functional' ...
0334       '\n# 4 : First functional' ...
0335       '\n# 5 : Standard space template' ...
0336       '\nset fmri(bgimage) %d\n'], fsf.bgimage);
0337 fprintf(fid,'%s', fsf_str);
0338 
0339 if fsf.version == 5.98
0340   fsf_str = sprintf([...
0341       '\n# Create time series plots' ...
0342       '\nset fmri(tsplot_yn) %d\n'], fsf.tsplot_yn);
0343   fprintf(fid,'%s', fsf_str);
0344 end
0345 
0346 fsf_str = sprintf([...
0347       '\n# Registration?' ...
0348       '\nset fmri(reg_yn) %d\n'], fsf.reg_yn);
0349 fprintf(fid,'%s', fsf_str);
0350 
0351 fsf_str = sprintf([... 
0352       '\n# B0 fieldmap unwarping?' ...
0353       '\nset fmri(regunwarp_yn) %d\n'], fsf.regunwarp_yn);
0354 fprintf(fid,'%s', fsf_str);
0355 
0356 if fsf.version == 5.98
0357   fsf_str = sprintf([...
0358       '\n# EPI dwell time (ms)' ...
0359       '\nset fmri(dwell) %d\n'], fsf.dwell);
0360   fprintf(fid,'%s', fsf_str);
0361 
0362   fsf_str = sprintf([...
0363       '\n# EPI TE (ms)' ...
0364       '\nset fmri(te) %d\n'], fsf.te);
0365   fprintf(fid,'%s', fsf_str);
0366 
0367   fsf_str = sprintf([...
0368       '\n# % Signal loss threshold' ...
0369       '\nset fmri(signallossthresh) %d\n'], fsf.signallossthresh);
0370   fprintf(fid,'%s', fsf_str);
0371 
0372   fsf_str = sprintf([...
0373       '\n# Unwarp direction' ...
0374       '\nset fmri(unwarp_dir) %s\n'], fsf.unwarp_dir);
0375   fprintf(fid,'%s', fsf_str);
0376 end
0377 
0378 if fsf.version == 5.4
0379   fsf_str = sprintf([...
0380         '\n# Dwell/Asymmetry ratio ' ...
0381         '\nset fmri(dwellasym) %d\n'], fsf.dwellasym);
0382   fprintf(fid,'%s', fsf_str);
0383 end
0384 
0385 fsf_str = sprintf([...
0386       '\n# Registration to initial structural' ...
0387       '\nset fmri(reginitial_highres_yn) %d\n'], fsf.reginitial_highres_yn);
0388 fprintf(fid,'%s', fsf_str);
0389 
0390 fsf_str = sprintf([...
0391       '\n# Search space for registration to initial structural' ...
0392       '\n# 0   : No search' ...
0393       '\n# 90  : Normal search' ...
0394       '\n# 180 : Full search' ...
0395       '\nset fmri(reginitial_highres_search) %d\n'], fsf.reginitial_highres_search);
0396 fprintf(fid,'%s', fsf_str);
0397 
0398 fsf_str = sprintf([...
0399       '\n# Degrees of Freedom for registration to initial structural' ...
0400       '\nset fmri(reginitial_highres_dof) %d\n'], fsf.reginitial_highres_dof);
0401 fprintf(fid,'%s', fsf_str);
0402 
0403 if fsf.version == 5.4
0404   fsf_str = sprintf([...
0405         '\n# Do nonlinear registration to initial structural?' ...
0406         '\nset fmri(reginitial_highres_nonlinear_yn) %d\n'], fsf.reginitial_highres_nonlinear_yn);
0407   fprintf(fid,'%s', fsf_str);
0408 end
0409 
0410 fsf_str = sprintf([...
0411       '\n# Registration to main structural' ...
0412       '\nset fmri(reghighres_yn) %d\n'], fsf.reghighres_yn);
0413 fprintf(fid,'%s', fsf_str);
0414 
0415 fsf_str = sprintf([...
0416       '\n# Search space for registration to main structural' ...
0417       '\n# 0   : No search' ...
0418       '\n# 90  : Normal search' ...
0419       '\n# 180 : Full search' ...
0420       '\nset fmri(reghighres_search) %d\n'], fsf.reghighres_search);
0421 fprintf(fid,'%s', fsf_str);
0422 
0423 fsf_str = sprintf([...
0424       '\n# Degrees of Freedom for registration to main structural' ...
0425       '\nset fmri(reghighres_dof) %d\n'], fsf.reghighres_dof);
0426 fprintf(fid,'%s', fsf_str);
0427 
0428 if fsf.version == 5.4
0429   fsf_str = sprintf([...
0430         '\n# Do nonlinear registration to main structural?' ...
0431         '\nset fmri(reghighres_nonlinear_yn) %d\n'], fsf.reghighres_nonlinear_yn);
0432   fprintf(fid,'%s', fsf_str);
0433 end
0434 
0435 fsf_str = sprintf([...
0436       '\n# Registration to standard image?' ...
0437       '\nset fmri(regstandard_yn) %d\n'], fsf.regstandard_yn);
0438 fprintf(fid,'%s', fsf_str);
0439 
0440 fsf_str = sprintf([...
0441       '\n# Standard image' ...
0442       '\nset fmri(regstandard) "%s"\n'], fsf.regstandard);
0443 fprintf(fid,'%s', fsf_str);
0444 
0445 fsf_str = sprintf([...
0446       '\n# Search space for registration to standard space' ...
0447       '\n# 0   : No search' ...
0448       '\n# 90  : Normal search' ...
0449       '\n# 180 : Full search' ...
0450       '\nset fmri(regstandard_search) %d\n'], fsf.regstandard_search);
0451 fprintf(fid,'%s', fsf_str);
0452 
0453 if fsf.version == 5.98
0454   fsf_str = sprintf([...
0455       '\n# Control nonlinear warp field resolution' ...
0456       '\nset fmri(regstandard_nonlinear_warpres) %d\n'],...
0457       fsf.regstandard_nonlinear_warpres);
0458   fprintf(fid,'%s', fsf_str);
0459 end
0460 
0461 fsf_str = sprintf([...
0462       '\n# Degrees of Freedom for registration to standard space' ...
0463       '\nset fmri(regstandard_dof) %d\n'], fsf.regstandard_dof);
0464 fprintf(fid,'%s', fsf_str);
0465 
0466 fsf_str = sprintf([...
0467       '\n# Do nonlinear registration to standard space?' ...
0468       '\nset fmri(regstandard_nonlinear_yn) %d\n'], fsf.regstandard_nonlinear_yn);
0469 fprintf(fid,'%s', fsf_str);
0470 
0471 fsf_str = sprintf([...
0472       '\n# High pass filter cutoff' ...
0473       '\nset fmri(paradigm_hp) %d\n'], fsf.paradigm_hp);
0474 fprintf(fid,'%s', fsf_str);
0475 
0476 fsf_str = sprintf([...
0477       '\n# Number of lower-level copes feeding into higher-level analysis' ...
0478       '\nset fmri(ncopeinputs) %d\n'], fsf.ncopeinputs);
0479 fprintf(fid,'%s', fsf_str);
0480 
0481 nfiles = length(fsf.feat_files);
0482 for ifile = 1:nfiles
0483   fsf_str = sprintf([...
0484     '\n# 4D AVW data or FEAT directory (%d)' ...
0485     '\nset feat_files(%d) "%s"\n'], ifile, ifile, fsf.feat_files{ifile});
0486   fprintf(fid,'%s', fsf_str);
0487 end
0488 
0489 if fsf.reginitial_highres_yn
0490   nfiles = length(fsf.initial_highres_files);
0491   for ifile = 1:nfiles
0492     fsf_str = sprintf([...
0493       '\n# Session''s structural image for analysis %d' ...
0494       '\nset initial_highres_files(%d) "%s"\n'], ...
0495     ifile, ifile, fsf.initial_highres_files{ifile});
0496     fprintf(fid,'%s', fsf_str);
0497   end
0498 end
0499 
0500 if fsf.reghighres_yn
0501   nfiles = length(fsf.highres_files);
0502   for ifile = 1:nfiles
0503     fsf_str = sprintf([...
0504       '\n# Subject''s structural image for analysis %d' ...
0505       '\nset highres_files(%d) "%s"\n'], ifile, ifile, fsf.highres_files{ifile});
0506     fprintf(fid,'%s', fsf_str);  
0507   end
0508 end
0509   
0510 % Here we loop over all of the variables specified in the model
0511 nev = length(fsf.ev);
0512 for iev = 1:nev
0513   ev = fsf.ev(iev);
0514 
0515   if fsf.version == 5.98
0516     fsf_str = sprintf([...
0517         '\n# EV %d title' ...
0518         '\nset fmri(evtitle%d) "%s"\n'], iev, iev, ev.name);
0519     fprintf(fid,'%s', fsf_str);
0520   end
0521   
0522   fsf_str = sprintf([...
0523     '\n# Basic waveform shape (EV %d)' ...
0524     '\n# 0 : Square' ...
0525     '\n# 1 : Sinusoid' ... 
0526     '\n# 2 : Custom (1 entry per volume)' ...
0527     '\n# 3 : Custom (3 column format)' ...
0528     '\n# 4 : Interaction' ...
0529     '\nset fmri(shape%d) %d\n'], iev, iev, ev.shape);
0530   fprintf(fid,'%s', fsf_str);
0531   
0532   fsf_str = sprintf([...
0533     '\n# Convolution (EV %d)' ...
0534     '\n# 0 : None' ...
0535     '\n# 1 : Gaussian' ...
0536     '\n# 2 : Gamma' ...
0537     '\n# 3 : Double-Gamma HRF' ...
0538     '\n# 4 : Gamma basis functions' ...
0539     '\n# 5 : Sine basis functions' ...
0540     '\n# 6 : FIR basis functions' ...
0541     '\nset fmri(convolve%d) %d\n'], iev, iev, ev.convolve);
0542   fprintf(fid,'%s', fsf_str);
0543 
0544   fsf_str = sprintf([...
0545     '\n# Convolve phase (EV %d)' ...
0546     '\nset fmri(convolve_phase%d) %d\n'], iev, iev, ev.convolve);
0547   fprintf(fid,'%s', fsf_str);
0548   
0549   fsf_str = sprintf([...
0550     '\n# Apply temporal filtering (EV %d)' ...
0551     '\nset fmri(tempfilt_yn%d) %d\n'], iev, iev, ev.tempfilt_yn);
0552   fprintf(fid,'%s', fsf_str);
0553   
0554   fsf_str = sprintf([...
0555     '\n# Add temporal derivative (EV %d)' ...
0556     '\nset fmri(deriv_yn%d) %d\n'], iev, iev, ev.deriv_yn);
0557   fprintf(fid,'%s', fsf_str);
0558   
0559   switch ev.shape
0560     case 0
0561       fsf_str = sprintf([...
0562         '\n# Skip (EV %d)' ...
0563         '\nset fmri(skip%d) %d\n'], iev, iev, ev.skip);
0564       fprintf(fid,'%s', fsf_str);
0565       
0566       fsf_str = sprintf([...
0567         '\n# Off (EV %d)' ...
0568         '\nset fmri(off%d) %1.2f\n'], iev, iev, ev.off);
0569       fprintf(fid,'%s', fsf_str);
0570       
0571       fsf_str = sprintf([...
0572         '\n# On (EV %d)' ...
0573         '\nset fmri(on%d) %1.2f\n'], iev, iev, ev.on);
0574       fprintf(fid,'%s', fsf_str);
0575       
0576       fsf_str = sprintf([...
0577         '\n# Phase (EV %d)' ...
0578         '\nset fmri(phase%d) %d\n'], iev, iev, ev.phase);
0579       fprintf(fid,'%s', fsf_str);
0580       
0581       fsf_str = sprintf([...
0582         '\n# Stop (EV %d)' ...
0583         '\nset fmri(stop%d) %d\n'], iev, iev, ev.stop);
0584       fprintf(fid,'%s', fsf_str);
0585     case {2,3}
0586       fsf_str = sprintf([...
0587         '\n# Custom EV file (EV %d)' ...
0588         '\nset fmri(custom%d) "%s"\n'], iev, iev, ev.fname);
0589       fprintf(fid,'%s', fsf_str);
0590     otherwise
0591       fprintf('Not set up to handle this EV shape yet\n');
0592   end % switch ev.shape
0593   
0594   % Add convolution info
0595   switch ev.convolve
0596     case 1  % gaussian
0597       fsf_str = sprintf([...
0598         '\n# Gauss sigma (EV %d)' ...
0599         '\nset fmri(gausssigma%d) %1.2f\n'], iev, iev, ev.gausssigma);
0600       fprintf(fid,'%s', fsf_str);
0601 
0602       fsf_str = sprintf([...
0603         '\n# Gauss delay (EV %d)' ...
0604         '\nset fmri(gaussdelay%d) %1.2f\n'], iev, iev, ev.gaussdelay);
0605       fprintf(fid,'%s', fsf_str);
0606       
0607   end
0608   
0609   
0610   % Add the orthogonalization info
0611   if ~isempty(ev.ortho)
0612     ortho_vect = [0 ev.ortho];
0613     for jev = 0:nev
0614       fsf_str = sprintf([...
0615         '\n# Orthogonalise EV %d wrt EV %d' ...
0616         '\nset fmri(ortho%d.%d) %d'], iev, jev, iev, jev, ortho_vect(jev+1));
0617       fprintf(fid,'%s', fsf_str);
0618     end % for jev
0619   end
0620 end % for iev
0621 
0622 % Add contrast information from fsf.con structure
0623 fsf_str = sprintf([...
0624       '\n# Contrast & F-tests mode' ...
0625       '\n# real : control real EVs' ...
0626       '\n# orig : control original EVs' ...
0627       '\nset fmri(con_mode_old) %s' ...
0628       '\nset fmri(con_mode) %s'], fsf.con_mode_old, fsf.con_mode);
0629 fprintf(fid,'%s', fsf_str);
0630 
0631 % Loop over each of the real contrasts
0632 ncon = length(fsf.con);
0633 nFtest = length(fsf.Ftest);
0634 
0635 for icon = 1:ncon
0636   con = fsf.con(icon);
0637   
0638   mode = con.type;
0639   
0640   fsf_str = sprintf([...
0641     '\n# Display images for contrast_%s %d' ...
0642     '\nset fmri(conpic_%s.%d) %d\n'], mode, icon, mode, icon, con.conpic);
0643   fprintf(fid,'%s', fsf_str);
0644 
0645   fsf_str = sprintf([...
0646     '\n# Title for contrast_%s %d' ...
0647     '\nset fmri(conname_%s.%d) "%s"\n'], mode, icon, mode, icon, con.conname);
0648   fprintf(fid,'%s', fsf_str);
0649 
0650   for iev = 1:nev
0651     if length(con.con_vect) < iev, continue, end
0652     fsf_str = sprintf([...
0653       '\n# Real contrast_%s vector %d element %d' ...
0654       '\nset fmri(con_%s%d.%d) %d\n'], mode, icon, iev, mode, icon, iev, con.con_vect(iev));
0655     fprintf(fid,'%s', fsf_str);
0656   end % for iev
0657 
0658   for iftest = 1:length(con.ftest)
0659     fsf_str = sprintf([...
0660       '\n# F-test %d element %d' ...
0661       '\nset fmri(ftest_%s%d.%d) %d\n'], iftest, icon, mode, iftest, icon, con.ftest(iftest));
0662     fprintf(fid,'%s', fsf_str);
0663   end
0664 end % for icon=
0665 
0666 % Contrast masking
0667 fsf_str = sprintf([...
0668       '\n# Contrast masking - use >0 instead of thresholding?' ...
0669       '\nset fmri(conmask_zerothresh_yn) %d\n'], fsf.conmask_zerothresh_yn);
0670 fprintf(fid,'%s', fsf_str);
0671 
0672 fsf_str = sprintf([...
0673       '\n# Do contrast masking at all?' ...
0674       '\nset fmri(conmask1_1) %d\n'], fsf.conmask1_1);
0675 fprintf(fid,'%s', fsf_str);
0676 
0677 if fsf.version == 5.98
0678   % Extra non-GUI options
0679   fsf_str = sprintf([...
0680       '\n#############################################################' ...
0681       '\n# Now options that don''t appear in the GUI\n' ...
0682       '\n# Alternative example_func image (not derived from input 4D dataset' ...
0683       '\nset fmri(alternative_example_func) %s\n' ...
0684       '\n# Alternative (to BETting) mask image' ...
0685       '\nset fmri(alternative_mask) %s\n' ...
0686       '\n# Initial structural space registration initialisation transform' ...
0687       '\nset fmri(init_initial_highres) %s\n' ...
0688       '\n# Structural space registration initialisation transform' ...
0689       '\nset fmri(init_highres) %s\n' ...
0690       '\n# Standard space reigstration initialisation transform' ...
0691       '\nset fmri(init_standard) %s\n' ...
0692       '\n# For full FEAT analysis: overwrite .feat output dir?' ...
0693       '\nset fmri(overwrite_yn) %d\n'],...
0694       fsf.alternative_example_func,fsf.alternative_mask,...
0695       fsf.init_initial_highres,fsf.init_highres,...
0696       fsf.init_standard,fsf.overwrite_yn);
0697   fprintf(fid,'%s', fsf_str);
0698 end
0699 
0700 fclose(fid);
0701 return
0702 
0703 
0704 '\n# Mask real contrast/F-test 1 with real contrast/F-test 2?'
0705 'set fmri(conmask1_2) 0'
0706 
0707 '\n# Mask real contrast/F-test 1 with real contrast/F-test 3?'
0708 'set fmri(conmask1_3) 0'
0709 
0710 '\n# Mask real contrast/F-test 1 with real contrast/F-test 4?'
0711 'set fmri(conmask1_4) 0'
0712 
0713 '\n# Mask real contrast/F-test 2 with real contrast/F-test 1?'
0714 'set fmri(conmask2_1) 0'
0715 
0716 '\n# Mask real contrast/F-test 2 with real contrast/F-test 3?'
0717 'set fmri(conmask2_3) 0'
0718 
0719 '\n# Mask real contrast/F-test 2 with real contrast/F-test 4?'
0720 'set fmri(conmask2_4) 0'
0721 
0722 '\n# Mask real contrast/F-test 3 with real contrast/F-test 1?'
0723 'set fmri(conmask3_1) 0'
0724 
0725 '\n# Mask real contrast/F-test 3 with real contrast/F-test 2?'
0726 'set fmri(conmask3_2) 0'
0727 
0728 '\n# Mask real contrast/F-test 3 with real contrast/F-test 4?'
0729 'set fmri(conmask3_4) 0'
0730 
0731 '\n# Mask real contrast/F-test 4 with real contrast/F-test 1?'
0732 'set fmri(conmask4_1) 0'
0733 
0734 '\n# Mask real contrast/F-test 4 with real contrast/F-test 2?'
0735 'set fmri(conmask4_2) 0'
0736 
0737 '\n# Mask real contrast/F-test 4 with real contrast/F-test 3?'
0738 'set fmri(conmask4_3) 0'
0739

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