design.fsf 9.5 KB

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  1. # FEAT version number
  2. set fmri(version) 6.00
  3. # Are we in MELODIC?
  4. set fmri(inmelodic) 0
  5. # Analysis level
  6. # 1 : First-level analysis
  7. # 2 : Higher-level analysis
  8. set fmri(level) 2
  9. # Which stages to run
  10. # 0 : No first-level analysis (registration and/or group stats only)
  11. # 7 : Full first-level analysis
  12. # 1 : Pre-processing
  13. # 2 : Statistics
  14. set fmri(analysis) 2
  15. # Use relative filenames
  16. set fmri(relative_yn) 0
  17. # Balloon help
  18. set fmri(help_yn) 0
  19. # Run Featwatcher
  20. set fmri(featwatcher_yn) 0
  21. # Cleanup first-level standard-space images
  22. set fmri(sscleanup_yn) 0
  23. # Output directory
  24. set fmri(outputdir) "/data/project/studyforrest_ppa/sub-19/2nd-lvl_movie-ppa-grp"
  25. # TR(s)
  26. set fmri(tr) 3
  27. # Total volumes
  28. set fmri(npts) 8
  29. # Delete volumes
  30. set fmri(ndelete) 0
  31. # Perfusion tag/control order
  32. set fmri(tagfirst) 1
  33. # Number of first-level analyses
  34. set fmri(multiple) 8
  35. # Higher-level input type
  36. # 1 : Inputs are lower-level FEAT directories
  37. # 2 : Inputs are cope images from FEAT directories
  38. set fmri(inputtype) 1
  39. # Carry out pre-stats processing?
  40. set fmri(filtering_yn) 0
  41. # Brain/background threshold, %
  42. set fmri(brain_thresh) 10
  43. # Critical z for design efficiency calculation
  44. set fmri(critical_z) 5.3
  45. # Noise level
  46. set fmri(noise) 0.66
  47. # Noise AR(1)
  48. set fmri(noisear) 0.34
  49. # Motion correction
  50. # 0 : None
  51. # 1 : MCFLIRT
  52. set fmri(mc) 1
  53. # Spin-history (currently obsolete)
  54. set fmri(sh_yn) 0
  55. # B0 fieldmap unwarping?
  56. set fmri(regunwarp_yn) 0
  57. # EPI dwell time (ms)
  58. set fmri(dwell) 0.7
  59. # EPI TE (ms)
  60. set fmri(te) 35
  61. # % Signal loss threshold
  62. set fmri(signallossthresh) 10
  63. # Unwarp direction
  64. set fmri(unwarp_dir) y-
  65. # Slice timing correction
  66. # 0 : None
  67. # 1 : Regular up (0, 1, 2, 3, ...)
  68. # 2 : Regular down
  69. # 3 : Use slice order file
  70. # 4 : Use slice timings file
  71. # 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
  72. set fmri(st) 0
  73. # Slice timings file
  74. set fmri(st_file) ""
  75. # BET brain extraction
  76. set fmri(bet_yn) 1
  77. # Spatial smoothing FWHM (mm)
  78. set fmri(smooth) 5
  79. # Intensity normalization
  80. set fmri(norm_yn) 0
  81. # Perfusion subtraction
  82. set fmri(perfsub_yn) 0
  83. # Highpass temporal filtering
  84. set fmri(temphp_yn) 1
  85. # Lowpass temporal filtering
  86. set fmri(templp_yn) 0
  87. # MELODIC ICA data exploration
  88. set fmri(melodic_yn) 0
  89. # Carry out main stats?
  90. set fmri(stats_yn) 1
  91. # Carry out prewhitening?
  92. set fmri(prewhiten_yn) 1
  93. # Add motion parameters to model
  94. # 0 : No
  95. # 1 : Yes
  96. set fmri(motionevs) 0
  97. set fmri(motionevsbeta) ""
  98. set fmri(scriptevsbeta) ""
  99. # Robust outlier detection in FLAME?
  100. set fmri(robust_yn) 0
  101. # Higher-level modelling
  102. # 3 : Fixed effects
  103. # 0 : Mixed Effects: Simple OLS
  104. # 2 : Mixed Effects: FLAME 1
  105. # 1 : Mixed Effects: FLAME 1+2
  106. set fmri(mixed_yn) 3
  107. # Number of EVs
  108. set fmri(evs_orig) 1
  109. set fmri(evs_real) 1
  110. set fmri(evs_vox) 0
  111. # Number of contrasts
  112. set fmri(ncon_orig) 1
  113. set fmri(ncon_real) 1
  114. # Number of F-tests
  115. set fmri(nftests_orig) 0
  116. set fmri(nftests_real) 0
  117. # Add constant column to design matrix? (obsolete)
  118. set fmri(constcol) 0
  119. # Carry out post-stats steps?
  120. set fmri(poststats_yn) 0
  121. # Pre-threshold masking?
  122. set fmri(threshmask) ""
  123. # Thresholding
  124. # 0 : None
  125. # 1 : Uncorrected
  126. # 2 : Voxel
  127. # 3 : Cluster
  128. set fmri(thresh) 3
  129. # P threshold
  130. set fmri(prob_thresh) 0.05
  131. # Z threshold
  132. set fmri(z_thresh) 3.4
  133. # Z min/max for colour rendering
  134. # 0 : Use actual Z min/max
  135. # 1 : Use preset Z min/max
  136. set fmri(zdisplay) 0
  137. # Z min in colour rendering
  138. set fmri(zmin) 2
  139. # Z max in colour rendering
  140. set fmri(zmax) 8
  141. # Colour rendering type
  142. # 0 : Solid blobs
  143. # 1 : Transparent blobs
  144. set fmri(rendertype) 1
  145. # Background image for higher-level stats overlays
  146. # 1 : Mean highres
  147. # 2 : First highres
  148. # 3 : Mean functional
  149. # 4 : First functional
  150. # 5 : Standard space template
  151. set fmri(bgimage) 1
  152. # Create time series plots
  153. set fmri(tsplot_yn) 0
  154. # Registration to initial structural
  155. set fmri(reginitial_highres_yn) 0
  156. # Search space for registration to initial structural
  157. # 0 : No search
  158. # 90 : Normal search
  159. # 180 : Full search
  160. set fmri(reginitial_highres_search) 90
  161. # Degrees of Freedom for registration to initial structural
  162. set fmri(reginitial_highres_dof) 3
  163. # Registration to main structural
  164. set fmri(reghighres_yn) 0
  165. # Search space for registration to main structural
  166. # 0 : No search
  167. # 90 : Normal search
  168. # 180 : Full search
  169. set fmri(reghighres_search) 90
  170. # Degrees of Freedom for registration to main structural
  171. set fmri(reghighres_dof) BBR
  172. # Registration to standard image?
  173. set fmri(regstandard_yn) 1
  174. # Use alternate reference images?
  175. set fmri(alternateReference_yn) 0
  176. # Standard image
  177. set fmri(regstandard) "/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain"
  178. # Search space for registration to standard space
  179. # 0 : No search
  180. # 90 : Normal search
  181. # 180 : Full search
  182. set fmri(regstandard_search) 90
  183. # Degrees of Freedom for registration to standard space
  184. set fmri(regstandard_dof) 12
  185. # Do nonlinear registration from structural to standard space?
  186. set fmri(regstandard_nonlinear_yn) 0
  187. # Control nonlinear warp field resolution
  188. set fmri(regstandard_nonlinear_warpres) 10
  189. # High pass filter cutoff
  190. set fmri(paradigm_hp) 100
  191. # Total voxels
  192. set fmri(totalVoxels) 111703680
  193. # Number of lower-level copes feeding into higher-level analysis
  194. set fmri(ncopeinputs) 10
  195. # Use lower-level cope 1 for higher-level analysis
  196. set fmri(copeinput.1) 1
  197. # Use lower-level cope 2 for higher-level analysis
  198. set fmri(copeinput.2) 1
  199. # Use lower-level cope 3 for higher-level analysis
  200. set fmri(copeinput.3) 1
  201. # Use lower-level cope 4 for higher-level analysis
  202. set fmri(copeinput.4) 1
  203. # Use lower-level cope 5 for higher-level analysis
  204. set fmri(copeinput.5) 1
  205. # Use lower-level cope 6 for higher-level analysis
  206. set fmri(copeinput.6) 1
  207. # Use lower-level cope 7 for higher-level analysis
  208. set fmri(copeinput.7) 1
  209. # Use lower-level cope 8 for higher-level analysis
  210. set fmri(copeinput.8) 1
  211. # Use lower-level cope 9 for higher-level analysis
  212. set fmri(copeinput.9) 1
  213. # Use lower-level cope 10 for higher-level analysis
  214. set fmri(copeinput.10) 1
  215. # 4D AVW data or FEAT directory (1)
  216. set feat_files(1) "/data/project/studyforrest_ppa/sub-19/run-1_movie-ppa-grp.feat"
  217. # 4D AVW data or FEAT directory (2)
  218. set feat_files(2) "/data/project/studyforrest_ppa/sub-19/run-2_movie-ppa-grp.feat"
  219. # 4D AVW data or FEAT directory (3)
  220. set feat_files(3) "/data/project/studyforrest_ppa/sub-19/run-3_movie-ppa-grp.feat"
  221. # 4D AVW data or FEAT directory (4)
  222. set feat_files(4) "/data/project/studyforrest_ppa/sub-19/run-4_movie-ppa-grp.feat"
  223. # 4D AVW data or FEAT directory (5)
  224. set feat_files(5) "/data/project/studyforrest_ppa/sub-19/run-5_movie-ppa-grp.feat"
  225. # 4D AVW data or FEAT directory (6)
  226. set feat_files(6) "/data/project/studyforrest_ppa/sub-19/run-6_movie-ppa-grp.feat"
  227. # 4D AVW data or FEAT directory (7)
  228. set feat_files(7) "/data/project/studyforrest_ppa/sub-19/run-7_movie-ppa-grp.feat"
  229. # 4D AVW data or FEAT directory (8)
  230. set feat_files(8) "/data/project/studyforrest_ppa/sub-19/run-8_movie-ppa-grp.feat"
  231. # Add confound EVs text file
  232. set fmri(confoundevs) 0
  233. # EV 1 title
  234. set fmri(evtitle1) ""
  235. # Basic waveform shape (EV 1)
  236. # 0 : Square
  237. # 1 : Sinusoid
  238. # 2 : Custom (1 entry per volume)
  239. # 3 : Custom (3 column format)
  240. # 4 : Interaction
  241. # 10 : Empty (all zeros)
  242. set fmri(shape1) 2
  243. # Convolution (EV 1)
  244. # 0 : None
  245. # 1 : Gaussian
  246. # 2 : Gamma
  247. # 3 : Double-Gamma HRF
  248. # 4 : Gamma basis functions
  249. # 5 : Sine basis functions
  250. # 6 : FIR basis functions
  251. set fmri(convolve1) 0
  252. # Convolve phase (EV 1)
  253. set fmri(convolve_phase1) 0
  254. # Apply temporal filtering (EV 1)
  255. set fmri(tempfilt_yn1) 0
  256. # Add temporal derivative (EV 1)
  257. set fmri(deriv_yn1) 0
  258. # Custom EV file (EV 1)
  259. set fmri(custom1) "dummy"
  260. # Orthogonalise EV 1 wrt EV 0
  261. set fmri(ortho1.0) 0
  262. # Orthogonalise EV 1 wrt EV 1
  263. set fmri(ortho1.1) 0
  264. # Higher-level EV value for EV 1 and input 1
  265. set fmri(evg1.1) 1
  266. # Higher-level EV value for EV 1 and input 2
  267. set fmri(evg2.1) 1.0
  268. # Higher-level EV value for EV 1 and input 3
  269. set fmri(evg3.1) 1.0
  270. # Higher-level EV value for EV 1 and input 4
  271. set fmri(evg4.1) 1.0
  272. # Higher-level EV value for EV 1 and input 5
  273. set fmri(evg5.1) 1.0
  274. # Higher-level EV value for EV 1 and input 6
  275. set fmri(evg6.1) 1.0
  276. # Higher-level EV value for EV 1 and input 7
  277. set fmri(evg7.1) 1.0
  278. # Higher-level EV value for EV 1 and input 8
  279. set fmri(evg8.1) 1.0
  280. # Group membership for input 1
  281. set fmri(groupmem.1) 1
  282. # Group membership for input 2
  283. set fmri(groupmem.2) 1
  284. # Group membership for input 3
  285. set fmri(groupmem.3) 1
  286. # Group membership for input 4
  287. set fmri(groupmem.4) 1
  288. # Group membership for input 5
  289. set fmri(groupmem.5) 1
  290. # Group membership for input 6
  291. set fmri(groupmem.6) 1
  292. # Group membership for input 7
  293. set fmri(groupmem.7) 1
  294. # Group membership for input 8
  295. set fmri(groupmem.8) 1
  296. # Contrast & F-tests mode
  297. # real : control real EVs
  298. # orig : control original EVs
  299. set fmri(con_mode_old) real
  300. set fmri(con_mode) real
  301. # Display images for contrast_real 1
  302. set fmri(conpic_real.1) 1
  303. # Title for contrast_real 1
  304. set fmri(conname_real.1) "group mean"
  305. # Real contrast_real vector 1 element 1
  306. set fmri(con_real1.1) 1
  307. # Contrast masking - use >0 instead of thresholding?
  308. set fmri(conmask_zerothresh_yn) 0
  309. # Do contrast masking at all?
  310. set fmri(conmask1_1) 0
  311. ##########################################################
  312. # Now options that don't appear in the GUI
  313. # Alternative (to BETting) mask image
  314. set fmri(alternative_mask) ""
  315. # Initial structural space registration initialisation transform
  316. set fmri(init_initial_highres) ""
  317. # Structural space registration initialisation transform
  318. set fmri(init_highres) ""
  319. # Standard space registration initialisation transform
  320. set fmri(init_standard) ""
  321. # For full FEAT analysis: overwrite existing .feat output dir?
  322. set fmri(overwrite_yn) 1