afni.nimh.nih.gov
| January 23, 2023 10:36AM | |
Registered: 11 years ago Posts: 145 |
Hi everybody,
I have a problem which I've never seen before. I have the script below used to directly run 3dD.
For reasons I do not understand, the GLTs are producing three coefficient/tstat pairs of sub-briks per GLT. I've never seen this before. The output from 3dinfo showing below has been edited to remove sub-briks related to individual betas for brevity but I can provide the whole thing necessary.
The married regressors used in stim_times_AM1 regressors all contain only one married component, the delay.
Does anyone have any idea why what appears to me to be a straightforward 3dD woudl results in multiple GLTs for the same GLT spec?
I have a problem which I've never seen before. I have the script below used to directly run 3dD.
3dDeconvolve -input $fmriprepdir/sub-${subj}_ses-${ses}_task-CCT_run-*_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz \
-jobs 8 \
-polort 4 \
-float \
-jobs 10 \
-local_times \
-num_stimts 38 \
-allzero_OK \
-GOFORIT 3 \
-stim_times 1 $scriptdir/Error.txt 'BLOCK4(1,1)' \
-stim_label 1 Error \
-stim_times 2 $scriptdir/Feedback.txt 'BLOCK4(1,1)' \
-stim_label 2 Feedback \
-stim_times 3 $scriptdir/InitSpatialBranch.txt 'BLOCK4(1,1)' \
-stim_label 3 InitSpatialBranch \
-stim_times 4 $scriptdir/InitSpatialControl.txt 'BLOCK4(1,1)' \
-stim_label 4 InitSpatialControl \
-stim_times 5 $scriptdir/InitSpatialDelay.txt 'BLOCK4(1,1)' \
-stim_label 5 InitSpatialDelay \
-stim_times 6 $scriptdir/InitSpatialSwitch.txt 'BLOCK4(1,1)' \
-stim_label 6 InitSpatialSwitch \
-stim_times 7 $scriptdir/InitVerbalBranch.txt 'BLOCK4(1,1)' \
-stim_label 7 InitVerbalBranch \
-stim_times 8 $scriptdir/InitVerbalControl.txt 'BLOCK4(1,1)' \
-stim_label 8 InitVerbalControl \
-stim_times 9 $scriptdir/InitVerbalDelay.txt 'BLOCK4(1,1)' \
-stim_label 9 InitVerbalDelay \
-stim_times 10 $scriptdir/InitVerbalSwitch.txt 'BLOCK4(1,1)' \
-stim_label 10 InitVerbalSwitch \
-stim_times 11 $scriptdir/LeftResponse.txt 'BLOCK4(1,1)' \
-stim_label 11 LeftResponse \
-stim_times 12 $scriptdir/ReturnSpatialBranch.txt 'BLOCK4(1,1)' \
-stim_label 12 ReturnSpatialBranch \
-stim_times 13 $scriptdir/ReturnSpatialControl.txt 'BLOCK4(1,1)' \
-stim_label 13 ReturnSpatialControl \
-stim_times 14 $scriptdir/ReturnSpatialDelay.txt 'BLOCK4(1,1)' \
-stim_label 14 ReturnSpatialDelay \
-stim_times 15 $scriptdir/ReturnSpatialSwitch.txt 'BLOCK4(1,1)' \
-stim_label 15 ReturnSpatialSwitch \
-stim_times 16 $scriptdir/ReturnVerbalBranch.txt 'BLOCK4(1,1)' \
-stim_label 16 ReturnVerbalBranch \
-stim_times 17 $scriptdir/ReturnVerbalControl.txt 'BLOCK4(1,1)' \
-stim_label 17 ReturnVerbalControl \
-stim_times 18 $scriptdir/ReturnVerbalDelay.txt 'BLOCK4(1,1)' \
-stim_label 18 ReturnVerbalDelay \
-stim_times 19 $scriptdir/ReturnVerbalSwitch.txt 'BLOCK4(1,1)' \
-stim_label 19 ReturnVerbalSwitch \
-stim_times 20 $scriptdir/RightResponse.txt 'BLOCK4(1,1)' \
-stim_label 20 RightResponse \
-stim_times 21 $scriptdir/spatialBaseline1_tran.txt 'BLOCK4(1,1)' \
-stim_label 21 spatialBaseline1tran \
-stim_times 22 $scriptdir/spatialBaseline2_tran.txt 'BLOCK4(1,1)' \
-stim_label 22 spatialBaseline2tran \
-stim_times_AM1 23 $scriptdir/SpatialBranch.txt 'dmBLOCK(1)' \
-stim_label 23 SpatialBranch \
-stim_times_AM1 24 $scriptdir/SpatialControl.txt 'dmBLOCK(1)' \
-stim_label 24 SpatialControl \
-stim_times_AM1 25 $scriptdir/SpatialDelay.txt 'dmBLOCK(1)' \
-stim_label 25 SpatialDelay \
-stim_times 26 $scriptdir/spatialInit.txt 'BLOCK4(1,1)' \
-stim_label 26 spatialInit \
-stim_times_AM1 27 $scriptdir/SpatialSwitch.txt 'dmBLOCK(1)' \
-stim_label 27 SpatialSwitch \
-stim_times 28 $scriptdir/verbalBaseline1_tran.txt 'BLOCK4(1,1)' \
-stim_label 28 verbalBaseline1tran \
-stim_times 29 $scriptdir/verbalBaseline2_tran.txt 'BLOCK4(1,1)' \
-stim_label 29 verbalBaseline2tran \
-stim_times_AM1 30 $scriptdir/VerbalBranch.txt 'dmBLOCK(1)' \
-stim_label 30 VerbalBranch \
-stim_times_AM1 31 $scriptdir/VerbalControl.txt 'dmBLOCK(1)' \
-stim_label 31 VerbalControl \
-stim_times_AM1 32 $scriptdir/VerbalDelay.txt 'dmBLOCK(1)' \
-stim_label 32 VerbalDelay \
-stim_times 33 $scriptdir/verbalInit.txt 'BLOCK4(1,1)' \
-stim_label 33 verbalInit \
-stim_times_AM1 34 $scriptdir/VerbalSwitch.txt 'dmBLOCK(1)' \
-stim_label 34 VerbalSwitch \
-stim_times_AM1 35 $scriptdir/spatialBaseline1_sus.txt 'dmBLOCK(1)' \
-stim_label 35 spatialBaseline1sus \
-stim_times_AM1 36 $scriptdir/spatialBaseline2_sus.txt 'dmBLOCK(1)' \
-stim_label 36 spatialBaseline2sus \
-stim_times_AM1 37 $scriptdir/verbalBaseline1_sus.txt 'dmBLOCK(1)' \
-stim_label 37 verbalBaseline1sus \
-stim_times_AM1 38 $scriptdir/verbalBaseline2_sus.txt 'dmBLOCK(1)' \
-stim_label 38 verbalBaseline2sus \
-num_glt 5 \
-gltsym 'SYM: 0.25*SpatialBranch +0.25*SpatialDelay +0.25*VerbalBranch \
+.25*VerbalDelay -.25*SpatialControl -.25*SpatialSwitch -.25*VerbalControl \
-.25*VerbalSwitch' \
-glt_label 1 Positive_TC \
-gltsym 'SYM: +.25*SpatialBranch +.25*SpatialSwitch +.25*VerbalBranch \
+.25*VerbalSwitch -.25*SpatialControl -.25*SpatialDelay -.25*VerbalControl \
-.25*VerbalDelay' \
-glt_label 2 Positive_CC \
-gltsym 'SYM: +.167*SpatialBranch +.167*SpatialSwitch +.167*SpatialDelay \
+.167*VerbalBranch +.167*VerbalSwitch +.167*VerbalDelay -.5*SpatialControl \
-.5*VerbalControl' \
-glt_label 3 Positive_SM \
-gltsym 'SYM: +.25*SpatialBranch +.25*SpatialSwitch +.25*SpatialControl \
+.25*SpatialDelay -.25*VerbalBranch -.25*VerbalSwitch -.25*VerbalControl \
-.25*VerbalDelay' \
-glt_label 4 Spatial \
-gltsym 'SYM: +.25*VerbalBranch +.25*VerbalSwitch +.25*VerbalControl \
+.25*VerbalDelay -.25*SpatialBranch -.25*SpatialSwitch -.25*SpatialControl \
-.25*SpatialDelay' \
-glt_label 5 Verbal \
-fout -tout \
-x1D $output_dir/X.xmat.1D \
-xjpeg $output_dir/X.jpg \
-errts $output_dir/sub-${subj}_ses-${ses}_CCT_errts.nii \
-bucket $output_dir/sub-${subj}_ses-${ses}_CCT_stats.nii
For reasons I do not understand, the GLTs are producing three coefficient/tstat pairs of sub-briks per GLT. I've never seen this before. The output from 3dinfo showing below has been edited to remove sub-briks related to individual betas for brevity but I can provide the whole thing necessary.
++ 3dinfo: AFNI version=AFNI_22.3.06 (Nov 20 2022) [64-bit]
Dataset File: /home/colmconn/mriAnalysis/jess/sub-103_ses-V1_CCT_stats.nii
Identifier Code: AFN_b0UAV__ll21rc2QYrjXHDQ Creation Date: Thu Jan 19 11:27:08 2023
Template Space: MNI
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 541,577,400 (542 million) 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) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
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 = 150
<--- >8 ---->
-- At sub-brick #115 'Positive_TC_GLT#0_Coef' datum type is float: -25.3866 to 25.5636
-- At sub-brick #116 'Positive_TC_GLT#0_Tstat' datum type is float: -4.69123 to 5.50368
statcode = fitt; statpar = 1648
-- At sub-brick #117 'Positive_TC_GLT#1_Coef' datum type is float: -13.3206 to 20.6431
-- At sub-brick #118 'Positive_TC_GLT#1_Tstat' datum type is float: -6.19946 to 4.79392
statcode = fitt; statpar = 1648
-- At sub-brick #119 'Positive_TC_GLT#2_Coef' datum type is float: -7.33805 to 9.86096
-- At sub-brick #120 'Positive_TC_GLT#2_Tstat' datum type is float: -5.09876 to 4.80523
statcode = fitt; statpar = 1648
-- At sub-brick #121 'Positive_TC_GLT_Fstat' datum type is float: 0 to 34.4997
statcode = fift; statpar = 3 1648
-- At sub-brick #122 'Positive_CC_GLT#0_Coef' datum type is float: -27.425 to 29.315
-- At sub-brick #123 'Positive_CC_GLT#0_Tstat' datum type is float: -5.28585 to 5.24339
statcode = fitt; statpar = 1648
-- At sub-brick #124 'Positive_CC_GLT#1_Coef' datum type is float: -13.9727 to 23.5768
-- At sub-brick #125 'Positive_CC_GLT#1_Tstat' datum type is float: -4.90869 to 5.40784
statcode = fitt; statpar = 1648
-- At sub-brick #126 'Positive_CC_GLT#2_Coef' datum type is float: -7.86648 to 14.8651
-- At sub-brick #127 'Positive_CC_GLT#2_Tstat' datum type is float: -5.388 to 5.62748
statcode = fitt; statpar = 1648
-- At sub-brick #128 'Positive_CC_GLT_Fstat' datum type is float: 0 to 33.3531
statcode = fift; statpar = 3 1648
-- At sub-brick #129 'Positive_SM_GLT#0_Coef' datum type is float: -18.169 to 17.1799
-- At sub-brick #130 'Positive_SM_GLT#0_Tstat' datum type is float: -4.6474 to 4.97804
statcode = fitt; statpar = 1648
-- At sub-brick #131 'Positive_SM_GLT#1_Coef' datum type is float: -20.0609 to 13.8209
-- At sub-brick #132 'Positive_SM_GLT#1_Tstat' datum type is float: -11.5391 to 9.04824
statcode = fitt; statpar = 1648
-- At sub-brick #133 'Positive_SM_GLT#2_Coef' datum type is float: -18.2493 to 39.772
-- At sub-brick #134 'Positive_SM_GLT#2_Tstat' datum type is float: -5.01106 to 4.82161
statcode = fitt; statpar = 1648
-- At sub-brick #135 'Positive_SM_GLT_Fstat' datum type is float: 0 to 52.3296
statcode = fift; statpar = 3 1648
-- At sub-brick #136 'Spatial_GLT#0_Coef' datum type is float: -29.6044 to 20.976
-- At sub-brick #137 'Spatial_GLT#0_Tstat' datum type is float: -4.69783 to 6.55785
statcode = fitt; statpar = 1648
-- At sub-brick #138 'Spatial_GLT#1_Coef' datum type is float: -20.3043 to 23.3449
-- At sub-brick #139 'Spatial_GLT#1_Tstat' datum type is float: -8.70796 to 5.90311
statcode = fitt; statpar = 1648
-- At sub-brick #140 'Spatial_GLT#2_Coef' datum type is float: -7.86648 to 14.8651
-- At sub-brick #141 'Spatial_GLT#2_Tstat' datum type is float: -5.388 to 5.62748
statcode = fitt; statpar = 1648
-- At sub-brick #142 'Spatial_GLT_Fstat' datum type is float: 0 to 63.0401
statcode = fift; statpar = 3 1648
-- At sub-brick #143 'Verbal_GLT#0_Coef' datum type is float: -31.8397 to 22.2809
-- At sub-brick #144 'Verbal_GLT#0_Tstat' datum type is float: -4.91587 to 5.84735
statcode = fitt; statpar = 1648
-- At sub-brick #145 'Verbal_GLT#1_Coef' datum type is float: -18.485 to 22.0382
-- At sub-brick #146 'Verbal_GLT#1_Tstat' datum type is float: -9.67806 to 5.67452
statcode = fitt; statpar = 1648
-- At sub-brick #147 'Verbal_GLT#2_Coef' datum type is float: -12.2403 to 13.4385
-- At sub-brick #148 'Verbal_GLT#2_Tstat' datum type is float: -5.15695 to 4.98863
statcode = fitt; statpar = 1648
-- At sub-brick #149 'Verbal_GLT_Fstat' datum type is float: 0 to 82.2836
statcode = fift; statpar = 3 1648
The married regressors used in stim_times_AM1 regressors all contain only one married component, the delay.
Does anyone have any idea why what appears to me to be a straightforward 3dD woudl results in multiple GLTs for the same GLT spec?
| Subject | Author | Posted |
|---|---|---|
|
Colm Connolly | January 23, 2023 10:36AM |
|
rick reynolds | January 23, 2023 12:09PM |
|
Colm Connolly | January 23, 2023 01:28PM |
|
rick reynolds | January 23, 2023 01:47PM |
