Here is everything that you requested. I do not see slow performance with the data from the bootcamp. You can download the data I am using from here:
https://utexas.box.com/s/7penj3t5k5w3p4ah6ipfxxlfbdbp9lgx (it is from FCP-INDI/CoRR)
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.4.0-66-generic
version: #74-Ubuntu SMP Wed Jan 27 22:54:38 UTC 2021
distribution: Ubuntu 20.04.2 LTS
number of CPUs: 24
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/cameron/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Feb 25 2021
: AFNI_21.0.12 'Titus'
AFNI_version.txt : AFNI_21.0.12, linux_ubuntu_16_64, Feb 25 2021
which python : /home/cameron/venvs/cpac/bin/python
python version : 3.8.5
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/cameron/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /home/cameron/venvs/cpac/lib/python3.8/site-packages/matplotlib/pyplot.py
-------------------------------- env vars --------------------------------
PATH = /home/cameron/venvs/cpac/bin:/home/cameron/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cameron/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/cameron/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.4 (amd64)
have Ubuntu system: Ubuntu 20.04.2 LTS
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Feb 25 2021
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
afni -no_detach -q -VAFNI_COMPRESSOR=
<BLANK>
afni -no_detach -q -VAFNI_DONT_USE_PIGZ=
<BLANK>
Still seeing the problem:
time ~/abin/3dROIstats -mask mask2.nii.gz func.nii.gz
File Sub-brick Mean_1
func.nii.gz 0[?] 9957.563410
func.nii.gz 1[?] 9947.920665
func.nii.gz 2[?] 9938.978018
func.nii.gz 3[?] 9942.901682
...
func.nii.gz 334[?] 10085.826948
func.nii.gz 335[?] 10079.657652
func.nii.gz 336[?] 10037.459720
func.nii.gz 337[?] 10058.559225
real 2m35.273s
user 2m21.209s
sys 0m13.998s
Now trying with bootcamp data ...
++ Compile date = Feb 25 2021 {AFNI_21.0.12:linux_ubuntu_16_64}
time ~/abin/3dROIstats -mask mask.auto.nii.gz epi_r1+orig.HEAD
File Sub-brick Mean_1
epi_r1+orig.HEAD 0[#0] 1541.724452
epi_r1+orig.HEAD 1[#1] 1380.877077
epi_r1+orig.HEAD 2[#2] 1340.660904
epi_r1+orig.HEAD 3[#3] 1339.089622
...
epi_r1+orig.HEAD 148[#148] 1334.726368
epi_r1+orig.HEAD 149[#149] 1333.623429
epi_r1+orig.HEAD 150[#150] 1332.642166
epi_r1+orig.HEAD 151[#151] 1334.085370
real 0m0.114s
user 0m0.065s
sys 0m0.049s
time ~/abin/3dROIstats -mask mask.auto.nii.gz LONG.nii.gz
File Sub-brick Mean_1
LONG.nii.gz 0[#0] 1541.724452
LONG.nii.gz 1[#1] 1380.877077
LONG.nii.gz 2[#2] 1340.660904
LONG.nii.gz 3[#3] 1339.089622
...
LONG.nii.gz 605[#149] 1333.623429
LONG.nii.gz 606[#150] 1332.642166
LONG.nii.gz 607[#151] 1334.085370
real 0m1.466s
user 0m1.398s
sys 0m0.068s
3dinfo epi_r1+orig.HEAD
++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]
Dataset File: epi_r1+orig
Identifier Code: AFN_1obeBrbaja6u2HfupnCFbA Creation Date: Thu Mar 18 14:28:42 2010
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 64,204,800 (64 million) bytes
Geometry String: "MATRIX(2.75,0,0,-112.6622,0,2.75,0,-122.7787,0,0,3,-17.65058):80,80,33"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -112.662 [R] -to- 104.588 [L] -step- 2.750 mm [ 80 voxels]
A-to-P extent: -122.779 [A] -to- 94.471 [P] -step- 2.750 mm [ 80 voxels]
I-to-S extent: -17.651 -to- 78.349 [S] -step- 3.000 mm [ 33 voxels]
Number of time steps = 152 Time step = 2.00000s Origin = 0.00000s Number time-offset slices = 33 Thickness = 3.000
-- At sub-brick #0 '#0' datum type is short: 0 to 3272
-- At sub-brick #1 '#1' datum type is short: 0 to 2924
-- At sub-brick #2 '#2' datum type is short: 0 to 2841
** For info on all 152 sub-bricks, use '3dinfo -verb' **
----- HISTORY -----
[rickr@manwe.nimh.nih.gov: Thu Mar 18 11:19:14 2010] 3dcopy epi_r1.nii FT_epi_r1
[rickr@manwe.nimh.nih.gov: Thu Mar 18 14:28:42 2010] 3dcopy FT_epi_r1+orig epi_r1
++ 3dinfo: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]
Dataset File: func.nii.gz
Identifier Code: NII_hDcnbsY6k2aQQvVLdGzh0w Creation Date: Wed Mar 3 20:39:20 2021
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 160,595,968 (161 million) bytes
Geometry String: "MATRIX(3.4375,0,0,-119.0361,0,-3.4375,0,65.85879,0,0,3.959766,-91.56892):64,64,29"
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: -119.036 [R] -to- 97.526 [L] -step- 3.438 mm [ 64 voxels]
A-to-P extent: -150.704 [A] -to- 65.859 [P] -step- 3.437 mm [ 64 voxels]
I-to-S extent: -91.569 -to- 19.305 [S] -step- 3.960 mm [ 29 voxels]
Number of time steps = 338 Time step = 1.75000s 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 338 sub-bricks, use '3dinfo -verb' **
Other than voxel size and number of TRs the main different in datasets is the data type and the range of values, lets make epi_r1 match func.nii.gz for those and see if it changes anything:
3dcalc -prefix epi_r1_float.nii.gz -a epi_r1 -expr '10000*a/2962' -datum float
time 3dROIstats -mask mask.auto.nii.gz epi_r1_float.nii.gz
File Sub-brick Mean_1
epi_r1_float.nii.gz 0[#0] 5205.011654
epi_r1_float.nii.gz 1[#1] 4661.975278
epi_r1_float.nii.gz 2[#2] 4526.201565
epi_r1_float.nii.gz 3[#3] 4520.896766
...
epi_r1_float.nii.gz 148[#148] 4506.165995
epi_r1_float.nii.gz 149[#149] 4502.442365
epi_r1_float.nii.gz 150[#150] 4499.129527
epi_r1_float.nii.gz 151[#151] 4504.001923
real 0m0.481s
user 0m0.457s
sys 0m0.024s
When I try to convert func.nii.gz to float, I get:
3dcalc -prefix func_short.nii.gz -a func.nii.gz -exp 'a' -datum short
++ 3dcalc: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: varying brick factors, writing NIfTI as float
++ Output dataset ./func_short.nii.gz
Could that be related to the problem
Thanks again for the help!
=cc
