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create_fsf

PURPOSE ^

Populates FEAT fsf structure with default values

SYNOPSIS ^

function fsf=create_fsf(varargin)

DESCRIPTION ^

 Populates FEAT fsf structure with default values

   fsf=create_fsf(varargin);

 creates a FEAT fsf structure with default values, for feat v5.4 or v5.98.
 default version is the latest supported version (v5.98), however, you
 can specify the version by using the 'version' argument
 
   e.g. fsf = create_fsf('version',5.4)
 
 INPUT
   varargin: key,value pairs to set given defaults
       'version' (default: 5.98) - possible values in [5.4 5.98]
 
 See also write_fsf

 04/22/05 PJ

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

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

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