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Sincerely, AFNI HQ

History of AFNI updates  

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September 23, 2021 05:16AM
Thanks Gang, a final question:

I ran 3dMVM using a merged 4D volume with the vbm-gray-matter-modulated volumes of all 1800 subjects:

3dinfo ../GM_mod_merg.nii.gz 
++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]

Dataset File:    ../GM_mod_merg.nii.gz
Identifier Code: NII_FIGEgKOgUVe0sJpMi6fe6A  Creation Date: Thu Sep 23 11:08:02 2021
Template Space:  TLRC
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   6,498,928,800 (6.5 billion) 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 time steps = 1800  Time step = 2.00000s  Origin = 0.00000s
  -- At sub-brick #0 '?' datum type is float
  -- At sub-brick #1 '?' datum type is float
  -- At sub-brick #2 '?' datum type is float
** For info on all 1800 sub-bricks, use '3dinfo -verb' **
As you can see it has 1800 sub-briks.

I then refered to each of these sub-briks in the mvm-table (yes, they are in the correct order):
[robka@localhost mvm_test]$ cat table_no_smooth.txt 
Subj PRS status InputFile
1001008 HighPRS status1../GM_mod_merg.nii.gz[0]
1001794 HighPRS status2 ../GM_mod_merg.nii.gz[1]
1005915 HighPRS status2 ../GM_mod_merg.nii.gz[2]
etc..
And I ran 3dMVM:
3dMVM -prefix results_no_smooth -dataTable @table_no_smooth.txt -mask ../GM_mask.nii.gz -resid resid_no_smooth -jobs 4 \
-bsVars "PRS*status"

I just don't understand the output. Usually I get a "results_no_smooth+tlrc." file(s). With 3 sub-briks: Factor1(PRS), Factor2(status) Factor3(Interaction) and the Intercept (4 sub-briks).
But when I run the above the resulting "results_no_smooth+tlrc." file(s) have 1804 sub-briks. I.e. all the subjects plus the stats. This has never happaned before. The only new thing is that I refer to a large 4D volume containing all data, instead of individual files like I usually do with smaller samples.
3dinfo results_no_smooth+tlrc.
++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]

Dataset File:    results_no_smooth+tlrc
Identifier Code: XYZ_DvVyj6f44Rr5K15d5G0OjC  Creation Date: 
Template Space:  TLRC
Dataset Type:    Func-Bucket (-fbuc)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   3,256,685,432 (3.3 billion) 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 = 1804
  -- At sub-brick #0 '(Intercept) F' datum type is short:            0 to         32767 [internal]
                                        [*   0.00305185]             0 to           100 [scaled]
     statcode = fift;  statpar = 1 1794
  -- At sub-brick #1 'PRS F' datum type is short:            0 to         32767 [internal]
                                [*  0.000654147]             0 to       21.4345 [scaled]
     statcode = fift;  statpar = 1 1794
  -- At sub-brick #2 'MDDstatus F' datum type is short:            0 to         32767 [internal]
                                      [*  0.000365401]             0 to       11.9731 [scaled]
     statcode = fift;  statpar = 2 1794
** For info on all 1804 sub-bricks, use '3dinfo -verb' **

Is this normal or something to worry about?
Thanks!
Subject Author Posted

Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

Robin September 14, 2021 09:36AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

Daniel Glen September 15, 2021 10:30AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

gang September 15, 2021 11:06AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

Peter Molfese September 15, 2021 11:50AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

Robin September 16, 2021 05:57AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

Robin September 17, 2021 07:14AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

gang September 20, 2021 10:42PM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

Robin September 23, 2021 05:16AM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

gang September 25, 2021 01:25PM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM) Attachments

Robin September 25, 2021 03:00PM

Re: Stats (e.g. 3dMVM) on anatomical data (e..g VBM)

gang September 25, 2021 09:27PM