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Sincerely, AFNI HQ

History of AFNI updates  

|
April 02, 2019 10:23PM
Hello,

we obviously already miss the AFNI bootcamp!
What am I trying to do: run 3dttest++ with an anatomical mask on bilateral parietal lobes.
What error I get:
++ 3dttest++: AFNI version=AFNI_19.0.17 (Feb 22 2019) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as LONG form (label label dset label dset ...)
++ have 20 volumes corresponding to option '-setA'
++ 189973 voxels in -mask dataset
** FATAL ERROR: -mask doesn't match datasets number of voxels
** Program compile date = Feb 22 2019

I checked my stat.subject.HEAD files with 3dinfo and this is my output
++ 3dinfo: AFNI version=AFNI_19.0.17 (Feb 22 2019) [64-bit]

Dataset File:    stats.sub-011_REML+tlrc
Identifier Code: AFN_xXX_dIM3W6rsmxmGT1m_kQ  Creation Date: Mon Mar  4 13:54:55 2019
Template Space:  HaskinsPeds
Dataset Type:    Func-Bucket (-fbuc)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   283,948,280 (284 million) bytes
Geometry String: "MATRIX(-1.5,0,0,88.5,0,-1.5,0,125.5,0,0,1.5,-68.5):119,145,121"
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:   -88.500 [R] -to-    88.500 [L] -step-     1.500 mm [119 voxels]
A-to-P extent:   -90.500 [A] -to-   125.500 [P] -step-     1.500 mm [145 voxels]
I-to-S extent:   -68.500  -to-   111.500 [S] -step-     1.500 mm [121 voxels]

All my subjects are preprocessed to the Haskins_NL_template (below the preprocessing steps)

I then checked my mask:

++ 3dinfo: AFNI version=AFNI_19.0.17 (Feb 22 2019) [64-bit]

Dataset File:    anat_bilateral_parietal_mask+tlrc
Identifier Code: AFN_H9_F7DvqxfWaxI-hhtAu8Q  Creation Date: Tue Apr  2 14:44:25 2019
Template Space:  HaskinsPeds
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   7,102,004 (7.1 million) bytes
Geometry String: "MATRIX(-1,0,0,89,0,-1,0,126,0,0,1,-69):179,218,182"
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:   -89.000 [R] -to-    89.000 [L] -step-     1.000 mm [179 voxels]
A-to-P extent:   -91.000 [A] -to-   126.000 [P] -step-     1.000 mm [218 voxels]
I-to-S extent:   -69.000  -to-   112.000 [S] -step-     1.000 mm [182 voxels]


The mask has the same dimensions as the Haskins template I made it from but my subjects have different dimensions. I don't understand why my stats.subj files have 1.5 mm voxels and not 1mm like the template.
What am I missing here?

here it the preprocessing steps from the stats.subject file in case I made a mistake at some point.

HISTORY -----
[nens.lab@C07T20JBG1J2.local: Mon Mar  4 13:54:55 2019] Matrix source: ; 3dDeconvolve -input pb04.sub-011.r01.scale+tlrc.HEAD 
pb04.sub-011.r02.scale+tlrc.HEAD -censor censor_sub-011_combined_2.1D -ortvec mot_demean.r01.1D mot_demean_r01 
-ortvec mot_demean.r02.1D mot_demean_r02 -polort 2 -float -num_stimts 4 -stim_times 1 stimuli/Easy.tsv GAM 
-stim_label 1 LargeD -stim_times 2 stimuli/Medium.tsv GAM -stim_label 2 MediumD -stim_times 3 stimuli/Hard.tsv GAM 
-stim_label 3 SmallD -stim_times 4 stimuli/control_n.tsv GAM -stim_label 4 Ctrl_n -bout -jobs 4 -gltsym 'SYM: SmallD -LargeD' -glt_label 1 Small-Large 
-gltsym 'SYM: SmallD -MediumD' -glt_label 2 Small-Medium -gltsym 'SYM: MediumD -LargeD' -glt_label 3 Medium-Large 
-gltsym 'SYM: SmallD MediumD LargeD -3*Ctrl_n' -glt_label 4 All-control -gltsym 'SYM: LargeD -Ctrl_n' -glt_label 5 Large-Control 
-gltsym 'SYM: SmallD -Ctrl_n' -glt_label 6 Small-Control -gltsym 'SYM: MediumD -Ctrl_n' -glt_label 7 Medium-Control -fout -tout -x1D X.xmat.1D 
-xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub-011 -errts errts.sub-011 -bucket stats.sub-011
[nens.lab@C07T20JBG1J2.local: Mon Mar  4 13:54:55 2019] {AFNI_19.0.17:macos_10.12_local} 3dREMLfit -matrix X.xmat.1D 
-input 'pb04.sub-011.r01.scale+tlrc.HEAD pb04.sub-011.r02.scale+tlrc.HEAD' -fout -tout -Rbuck stats.sub-011_REML -Rvar stats.sub-011_REMLvar 
-Rfitts fitts.sub-011_REML -Rerrts errts.sub-011_REML -verb
[nens.lab@C07T20JBG1J2.local: Mon Mar  4 15:12:30 2019] {AFNI_19.0.17:macos_10.12_local} 3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:files_ClustSim/ClustSim.ACF.NN1_1sided.niml 
-atrstring AFNI_CLUSTSIM_MASK file:files_ClustSim/ClustSim.ACF.mask 
-atrstring AFNI_CLUSTSIM_NN2_1sided file:files_ClustSim/ClustSim.ACF.NN2_1sided.niml 
-atrstring AFNI_CLUSTSIM_NN3_1sided file:files_ClustSim/ClustSim.ACF.NN3_1sided.niml 
-atrstring AFNI_CLUSTSIM_NN1_2sided file:files_ClustSim/ClustSim.ACF.NN1_2sided.niml 
-atrstring AFNI_CLUSTSIM_NN2_2sided file:files_ClustSim/ClustSim.ACF.NN2_2sided.niml 
-atrstring AFNI_CLUSTSIM_NN3_2sided file:files_ClustSim/ClustSim.ACF.NN3_2sided.niml 
-atrstring AFNI_CLUSTSIM_NN1_bisided file:files_ClustSim/ClustSim.ACF.NN1_bisided.niml 
-atrstring AFNI_CLUSTSIM_NN2_bisided file:files_ClustSim/ClustSim.ACF.NN2_bisided.niml 
-atrstring AFNI_CLUSTSIM_NN3_bisided file:files_ClustSim/ClustSim.ACF.NN3_bisided.niml stats.sub-011+tlrc 
stats.sub-011_REML+tlrc

Finally, and not related, regarding the eBIDS, you should add a rating on quality, movement and whether participants were taken to the Rockbottom. smiling smiley
Subject Author Posted

Standardized EPI does not match wit anatomical mask from same template

Ilaria April 02, 2019 10:23PM

Re: Standardized EPI does not match wit anatomical mask from same template

Ilaria April 02, 2019 10:30PM

Re: Standardized EPI does not match wit anatomical mask from same template

ptaylor April 02, 2019 11:51PM

Re: Standardized EPI does not match wit anatomical mask from same template

Ilaria April 03, 2019 09:46PM

Re: Standardized EPI does not match wit anatomical mask from same template

ptaylor April 03, 2019 10:28PM