Hi, Gang (and others).
I'm an FSL user, but would like to use 3dLME to address some complex statistical models. I've been testing 3dLME, and have a few questions regarding input and output files.
1) What type of data is assumed to be in the input files for 3dLME? Are they beta-weights, and, if so, would the AFNI version of that be analogous to a cope file in FSL?
2) When I request that the output be in nifti format (by appending .nii to the prefix name), the program produces a single nifti file with just one volume. This isn't a problem b/c I can use 3dAFNItoNIFTI to create separate nifti files from each sub-brick in the default brick output. I just thought I'd let you know.
3) In the output brick there are a number of sub-bricks, some of which appear to be statistical tests, but others of which are not labeled. I've included a sample model and some 3dinfo output below. I assume that sub-bricks 0-3 (statcode = fift) are the statistics from the omnibus f-test (so, sub-bricks 1-3 are the f-statistics associated with the two main effects and the interaction, in that order, correct?). However, sub-bricks 4 and 5 both refer to a single contrast. I think sub-brick 5 is a map of z-statistics (statcode = fizt), but I don't know what sub-brick 4 is. Can you enlighten me?
Many thanks,
Ruskin
Model:
3dLME -prefix TEST_2/ESMF_3dLME_TEST_2_OUT_1 -jobs 24 \
-model "cond*group" \
-ranEff '~1' \
-SS_type 3 \
-num_glt 3 \
-gltLabel 1 'emot-shape' -gltCode 1 'cond : 1*emot -1*shape' \
-gltLabel 2 'emot' -gltCode 2 'cond : 1*emot ' \
-gltLabel 3 'shape' -gltCode 3 'cond : 1*shape' \
-dataTable \
Subj cond group InputFile \
s01 shape zero EST88302_00_zstat1_2mm.nii.gz \
...
3dinfo output:
++ 3dinfo: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
Dataset File: ESMF_3dLME_TEST_2_OUT_1+tlrc
Identifier Code: XYZ_Fex4BOPe9qKqA6Vezst81o Creation Date:
Template Space: MNI
Dataset Type: Func-Bucket (-fbuc)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 18,052,580 (18 million [mega]) bytes
Geometry String: "MATRIX(2,0,0,-90,0,-2,0,126,0,0,2,-72):91,109,91"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 2.000 mm [ 91 voxels]
A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 2.000 mm [109 voxels]
I-to-S extent: -72.000
-to- 108.000 [S] -step- 2.000 mm [ 91 voxels]
Number of values stored at each pixel = 10
-- At sub-brick #0 '(Intercept) F' datum type is short: 0 to 32767 [internal]
[* 0.00305185] 0 to 100 [scaled]
statcode = fift; statpar = 1 18
-- At sub-brick #1 'cond F' datum type is short: 0 to 32767 [internal]
[* 0.00305185] 0 to 100 [scaled]
statcode = fift; statpar = 1 18
-- At sub-brick #2 'group F' datum type is short: 0 to 32767 [internal]
[* 0.00100001] 0 to 32.7675 [scaled]
statcode = fift; statpar = 1 18
-- At sub-brick #3 'cond:group F' datum type is short: 0 to 32767 [internal]
[* 0.00104516] 0 to 34.2469 [scaled]
statcode = fift; statpar = 1 18
-- At sub-brick #4 'emot-shape' datum type is short: -11961 to 32767 [internal]
[* 0.000223776] -2.67659 to 7.33248 [scaled]
-- At sub-brick #5 'emot-shape Z' datum type is short: -13331 to 32767 [internal]
[* 0.00084621] -11.2808 to 27.7278 [scaled]
statcode = fizt
-- At sub-brick #6 'emot' datum type is short: -13896 to 32767 [internal]
[* 0.00028955] -4.02359 to 9.4877 [scaled]
-- At sub-brick #7 'emot Z' datum type is short: -21561 to 32767 [internal]
[* 0.000694567] -14.9756 to 22.7589 [scaled]
statcode = fizt
-- At sub-brick #8 'shape' datum type is short: -19488 to 32767 [internal]
[* 9.93517e-05] -1.93617 to 3.25546 [scaled]
-- At sub-brick #9 'shape Z' datum type is short: -22494 to 32767 [internal]
[* 0.000290856] -6.54252 to 9.53048 [scaled]
statcode = fizt
...
