Description of create

0001 function fsf=create_fsf(varargin)
0002 % Populates FEAT fsf structure with default values
0003 %
0004 %   fsf=create_fsf(varargin);
0005 %
0006 % creates a FEAT fsf structure with default values, for feat v5.4 or v5.98.
0007 % default version is the latest supported version (v5.98), however, you
0008 % can specify the version by using the 'version' argument
0009 %
0010 %   e.g. fsf = create_fsf('version',5.4)
0011 %
0012 % INPUT
0013 %   varargin: key,value pairs to set given defaults
0014 %       'version' (default: 5.98) - possible values in [5.4 5.98]
0015 %
0016 % See also write_fsf
0017 %
0018 % 04/22/05 PJ
0019 
0020 for ii=1:2:length(varargin)
0021   if ischar(varargin{ii})
0022     switch varargin{ii}
0023       case 'version'
0024         vers = varargin{ii+1};
0025       otherwise
0026         warning('unknown argument %s',varargin{ii});       
0027     end
0028   end
0029 end
0030 
0031 if ~exist('vers','var') || ~any(ismember([5.4 5.98],vers))
0032   vers = 5.98;
0033   warning('version set to %d',vers);
0034 end
0035 
0036 % FEAT version number
0037 fsf.version=vers;
0038 
0039 % Analysis level
0040 % 1 : First-level analysis
0041 % 2 : Higher-level analysis
0042 fsf.level=1;
0043 
0044 % Which stages to run
0045 % 0 : No first-level analysis (registration and/or group stats only)
0046 % 7 : Full first-level analysis
0047 % 1 : Pre-Stats
0048 % 3 : Pre-Stats + Stats
0049 % 2 :             Stats
0050 % % % % version 5.4
0051 % 6 :             Stats + Contrasts, Thresholding, Rendering
0052 % 4 :                     Contrasts, Thresholding, Rendering
0053 % % % % version 5.98
0054 % 6:              Stats + Post-Stats
0055 % 4:                      Post-Stats
0056 fsf.analysis=7;
0057 
0058 % Use relative filenames
0059 fsf.relative_yn=0;
0060 
0061 % Balloon help
0062 fsf.help_yn=1;
0063 
0064 % Run Featwatcher
0065 fsf.featwatcher_yn=1;
0066 
0067 % Cleanup first-level standard-space images
0068 fsf.sscleanup_yn=1;
0069 
0070 % Output directory
0071 fsf.outputdir='';
0072 
0073 % TR(s)
0074 fsf.tr=[];
0075 
0076 % Total volumes
0077 fsf.npts=[];
0078 
0079 % Delete volumes
0080 fsf.ndelete=0;
0081 
0082 % Number of first-level analyses
0083 fsf.multiple=1;  % Not a flag - actual num of analyses
0084 
0085 % Higher-level input type
0086 % 1 : Inputs are lower-level FEAT directories
0087 % 2 : Inputs are cope images from FEAT directories
0088 fsf.inputtype=1;
0089 
0090 % Carry out pre-stats processing?
0091 fsf.filtering_yn=1;
0092 
0093 % Brain/background threshold, %
0094 fsf.brain_thresh=10;
0095 
0096 % Post-stats-only directory copying
0097 % 0 : Overwrite original post-stats results
0098 % 1 : Copy original FEAT directory for new Contrasts, Thresholding, Rendering
0099 fsf.newdir_yn=0;
0100 
0101 % Slice timing correction
0102 % 0 : None
0103 % 1 : Regular up (0, 1, 2, 3, ...)
0104 % 2 : Regular down
0105 % 3 : Use slice order file
0106 % 4 : Use slice timings file
0107 % 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
0108 fsf.st=0;
0109 
0110 % Slice timings file
0111 fsf.st_file='';
0112 
0113 % Motion correction
0114 % 0 : None
0115 % 1 : MCFLIRT
0116 fsf.mc=1;
0117 
0118 % Spin-history (currently obsolete)
0119 fsf.sh_yn=0;
0120 
0121 % BET brain extraction
0122 fsf.bet_yn=1;
0123 
0124 % Spatial smoothing FWHM (mm)
0125 fsf.smooth=5;
0126 
0127 % Intensity normalization
0128 fsf.norm_yn=0;
0129 
0130 % Highpass temporal filtering
0131 fsf.temphp_yn=0;
0132 
0133 % Lowpass temporal filtering
0134 fsf.templp_yn=0;
0135 
0136 % MELODIC ICA data exploration
0137 fsf.melodic_yn=0;
0138 
0139 % Carry out main stats?
0140 fsf.stats_yn=1;
0141 
0142 % Carry out prewhitening?
0143 fsf.prewhiten_yn=1;
0144 
0145 % Higher-level modelling
0146 % 3 : Fixed effects
0147 % 0 : Mixed Effects: Simple OLS
0148 % 2 : Mixed Effects: FLAME (stage 1 only)
0149 % 1 : Mixed Effects: FLAME (full)
0150 fsf.mixed_yn=1;
0151 
0152 % Number of EVs
0153 fsf.evs_orig=0;
0154 fsf.evs_real=0;
0155 
0156 % Number of contrasts
0157 fsf.ncon_orig=0;
0158 fsf.ncon_real=0;
0159 
0160 % Number of F-tests
0161 fsf.nftests_orig=0;
0162 fsf.nftests_real=0;
0163 
0164 % Add constant column to design matrix? (obsolete)
0165 fsf.constcol=0;
0166 
0167 % Carry out post-stats steps?
0168 fsf.poststats_yn=1;
0169 
0170 % Pre-threshold masking?
0171 fsf.threshmask='';
0172 
0173 % Thresholding
0174 % 0 : None
0175 % 1 : Uncorrected
0176 % 2 : Voxel
0177 % 3 : Cluster
0178 fsf.thresh=3;
0179 
0180 % P threshold
0181 fsf.prob_thresh=0.05;
0182 
0183 % Z threshold
0184 fsf.z_thresh=2.3;
0185 
0186 % Z min/max for colour rendering
0187 % 0 : Use actual Z min/max
0188 % 1 : Use preset Z min/max
0189 fsf.zdisplay=0;
0190 
0191 % Z min in colour rendering
0192 fsf.zmin=1;
0193 
0194 % Z max in colour rendering
0195 fsf.zmax=15;
0196 
0197 % Colour rendering type
0198 % 0 : Solid blobs
0199 % 1 : Transparent blobs
0200 fsf.rendertype=1;
0201 
0202 % Background image for higher-level stats overlays
0203 % 1 : Mean highres
0204 % 2 : First highres
0205 % 3 : Mean functional
0206 % 4 : First functional
0207 % 5 : Standard space template
0208 fsf.bgimage=1;
0209 
0210 % Registration?
0211 fsf.reg_yn=1;
0212 
0213 % B0 fieldmap unwarping?
0214 fsf.regunwarp_yn=0;
0215 
0216 % Dwell/Asymmetry ratio
0217 fsf.dwellasym=-1;
0218 
0219 % Registration to initial structural
0220 fsf.reginitial_highres_yn=0;
0221 
0222 % Search space for registration to initial structural
0223 % 0   : No search
0224 % 90  : Normal search
0225 % 180 : Full search
0226 fsf.reginitial_highres_search=90;
0227 
0228 % Degrees of Freedom for registration to initial structural
0229 fsf.reginitial_highres_dof=12;
0230 
0231 % Registration to main structural
0232 fsf.reghighres_yn=0;
0233 
0234 % Search space for registration to main structural
0235 % 0   : No search
0236 % 90  : Normal search
0237 % 180 : Full search
0238 fsf.reghighres_search=90;
0239 
0240 % Degrees of Freedom for registration to main structural
0241 fsf.reghighres_dof=12;
0242 
0243 % Registration to standard image?
0244 fsf.regstandard_yn=1;
0245 
0246 % Standard image
0247 fsf.regstandard='/usr/local/fsl/etc/standard/avg152T1_brain.hdr';
0248 
0249 % Search space for registration to standard space
0250 % 0   : No search
0251 % 90  : Normal search
0252 % 180 : Full search
0253 fsf.regstandard_search=90;
0254 
0255 % Degrees of Freedom for registration to standard space
0256 fsf.regstandard_dof=12;
0257 
0258 % Do nonlinear registration to standard space?
0259 fsf.regstandard_nonlinear_yn=0;
0260 
0261 % High pass filter cutoff
0262 fsf.paradigm_hp=-1;
0263 
0264 % Number of lower-level copes feeding into higher-level analysis
0265 fsf.ncopeinputs=0;
0266 
0267 % 4D AVW data or FEAT directory (1)
0268 fsf.feat_files={};
0269 
0270 % Insert EV structure creation here
0271 fsf.ev = create_ev;
0272 
0273 fsf.con = [];  % create contrasts with create_con
0274 fsf.Ftest = [];  %
0275 
0276 % Contrast & F-tests mode
0277 % real : control real EVs
0278 % orig : control original EVs
0279 fsf.con_mode_old='orig';
0280 fsf.con_mode='orig';
0281 
0282 % Read in default contrast structures if desired
0283 
0284 % Contrast masking - use >0 instead of thresholding?
0285 fsf.conmask_zerothresh_yn=0;
0286 
0287 % This is an EV X EV matrix of what contrast should be masked with what.
0288 % Mask contrast index in row with contrast index in column
0289 % e.g. Mask real contrast/F-test 1 with real contrast/F-test 2?
0290 fsf.conmask_mtx = [];
0291 
0292 % Do contrast masking at all?
0293 fsf.conmask1_1=0;
0294 
0295 switch vers
0296   case 5.4
0297       
0298     % Delay before starting (hours)
0299     fsf.delay=0;
0300 
0301     % Do nonlinear registration to initial structural?
0302     fsf.reginitial_highres_nonlinear_yn=0;
0303 
0304     % Do nonlinear registration to main structural?
0305     fsf.reghighres_nonlinear_yn=0;
0306 
0307   case 5.98
0308       
0309     % Perfusion tag/control order
0310     fsf.tagfirst=1;
0311     
0312     % Critical z for design efficiency calculation
0313     fsf.critical_z = 5.3;
0314     
0315     % Noise level
0316     fsf.noise = 66;
0317     
0318     % Noise AR(1) (temporal smoothness
0319     fsf.noisear = 0.34;
0320     
0321     % EPI dwell time (ms)
0322     fsf.dwell = 0.7;
0323     
0324     % EPI TE (ms)
0325     fsf.te = 35;
0326     
0327     % Signal loss threshold
0328     fsf.signallossthresh = 10;
0329     
0330     % Unwarp direction
0331     fsf.unwarp_dir = 'y-';
0332     
0333     % Perfusion subtraction
0334     fsf.perfsub_yn = 0;
0335     
0336     % Add motion parameters to model
0337     % 0 : No
0338     % 1 : Yes
0339     fsf.motionevs = 0;
0340     
0341     % Robust outlier detection in FLAME?
0342     fsf.robust_yn = 0;
0343     
0344     % additional parameter for Number of EVs
0345     fsf.evs_vox = 0;
0346     
0347     % Create time series plots
0348     fsf.tsplot_yn = 0;
0349 
0350     % Control nonlinear warp field resolution
0351     fsf.regstandard_nonlinear_warpres = 10;
0352     
0353     % Add confound EVs text file
0354     fsf.confoundevs = 0;
0355     
0356     % Alternative example_func image (not derive from input 4D dataset)
0357     fsf.alternative_example_func = '';
0358     
0359     % Alternative (to BETting) mask image
0360     fsf.alternative_mask = '';
0361     
0362     % Initial structural space registration initialisation transform
0363     fsf.init_initial_highres = '';
0364     
0365     % Structural space reigstration initialisation transform
0366     fsf.init_highres = '';
0367     
0368     % Standard space reigstration initialisation transform
0369     fsf.init_standard = '';
0370     
0371     % For full FEAT analysis: overwrite existing .feat output dir?
0372     fsf.overwrite_yn = 0;
0373     
0374 end
create_fsf

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
