Dear FSFAST,
I am using the program selxavg3-sess on 3D data for a single session (i.e.
selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with
the following message:
OLS Residual Pass
run 1 t= 0.0
??? Error using ==> unknown
Out of memory. Type HELP MEMORY for your options.
Error in ==> fast_selxavg3 at 469
rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun;
I am using FSFAST v 5.1. My analysis uses FIR design, 6 runs in each
session with 18 contrasts. I executed the program on clusters 'launchpad'
(@ Martino's center) and allocated 49GB to it.
My question is how much CPU and memory you recommend I should
allocate? I have also attached the log file in this email.
Any help is greatly appreciated!
Thanks.
Wishes,
Tapsya
SCRIPT DIR :/space/adapt/1/users/tapsya/project_AVISI/
SCRIPT EXECUTED : Analysis_GLM_Volume.csh
SCRIPT EXECUTED BY :
tapsya
DATE EXECUTED :
Wed Aug 10 14:46:38 EDT 2011
--------------------------------------------------------------
selxavg3-sess logfile is /autofs/space/adapt_001/users/tapsya/project_AVISI/log/selxavg3-sess-bold-FIRsm6pf2.vol-110810144638.log
--------------------------------------------------------------
preproc-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -a FIRsm6pf2.vol -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
tapsya
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_1_0
setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/project_AVISI/
Linux compute-0-106.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
/autofs/space/adapt_001/users/tapsya/project_AVISI
/usr/local/freesurfer/stable5_1_0/fsfast/bin/preproc-sess
-s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -a FIRsm6pf2.vol -nolog
Wed Aug 10 14:46:44 EDT 2011
instem f
mc 1 f fmc
stc 1 fmc fmc.siemens
sm 1 fmc.siemens fmc.siemens.sm6
mask 1 brain
avml07 Template -----------------------------
mktemplate-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -rlf runlist -nolog -update
Session: /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07 ----------------
Wed Aug 10 14:46:45 EDT 2011
Detected input format at nii
avml07 Update not needed
Run: 002 ----------------
Wed Aug 10 14:46:46 EDT 2011
avml07 002 Update not needed
Run: 003 ----------------
Wed Aug 10 14:46:46 EDT 2011
avml07 003 Update not needed
Run: 005 ----------------
Wed Aug 10 14:46:46 EDT 2011
avml07 005 Update not needed
Run: 009 ----------------
Wed Aug 10 14:46:46 EDT 2011
avml07 009 Update not needed
Run: 010 ----------------
Wed Aug 10 14:46:47 EDT 2011
avml07 010 Update not needed
Run: 011 ----------------
Wed Aug 10 14:46:47 EDT 2011
avml07 011 Update not needed
Wed Aug 10 14:46:47 EDT 2011
mktemplate-sess completed
avml07 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -rlf runlist -nolog -update
------------------------------------------------
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07
Wed Aug 10 14:46:48 EDT 2011
avml07 Update not needed for session-level mask
avml07 Update not needed for run 002 mask
avml07 Update not needed for run 002 meanval
avml07 Update not needed for run 003 mask
avml07 Update not needed for run 003 meanval
avml07 Update not needed for run 005 mask
avml07 Update not needed for run 005 meanval
avml07 Update not needed for run 009 mask
avml07 Update not needed for run 009 meanval
avml07 Update not needed for run 010 mask
avml07 Update not needed for run 010 meanval
avml07 Update not needed for run 011 mask
avml07 Update not needed for run 011 meanval
Wed Aug 10 14:46:52 EDT 2011
mkbrainmask-sess done
avml07 Registration -----------------------------
register-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -dof 6 -rlf runlist -per-session -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Wed Aug 10 14:46:53 EDT 2011
setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/project_AVISI/
cd /autofs/space/adapt_001/users/tapsya/project_AVISI
/usr/local/freesurfer/stable5_1_0/fsfast/bin/register-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -dof 6 -rlf runlist -per-session -nolog -update
freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514
Linux compute-0-106.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
Session: /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07 ----------------
Wed Aug 10 14:46:53 EDT 2011
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07
Wed Aug 10 14:46:54 EDT 2011
register-sess completed
avml07 MC -----------------------------
mc-sess -fstem f -fmcstem fmc -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -rlf runlist -per-session -nolog -update
Logfile is /dev/null
-------------------------------------------
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07
RunList: 002 003 005 009 010 011
avml07 002 Update not needed
avml07 003 Update not needed
avml07 005 Update not needed
avml07 009 Update not needed
avml07 010 Update not needed
avml07 011 Update not needed
Wed Aug 10 14:46:56 EDT 2011
mc-sess completed SUCCESSFULLY
avml07 STC -----------------------------
stc-sess -i fmc -o fmc.siemens -so siemens -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -rlf runlist -nolog -update
Wed Aug 10 14:46:56 EDT 2011
/autofs/space/adapt_001/users/tapsya/project_AVISI
/usr/local/freesurfer/stable5_1_0/fsfast/bin/stc-sess
-i fmc -o fmc.siemens -so siemens -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -rlf runlist -nolog -update
$Id: stc-sess,v 1.10 2011/02/24 20:19:03 greve Exp $
compute-0-106.local
avml07 -----------------
Wed Aug 10 14:46:57 EDT 2011
-rw-rw-r-- 1 tapsya jackbgp 409397378 Aug 8 22:39 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/002/fmc.siemens.nii.gz
-rw-rw-r-- 1 tapsya jackbgp 403564510 Aug 8 21:56 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/002/fmc.nii.gz
Update not needed
-rw-rw-r-- 1 tapsya jackbgp 648266820 Aug 8 23:06 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/003/fmc.siemens.nii.gz
-rw-rw-r-- 1 tapsya jackbgp 634197919 Aug 8 22:04 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/003/fmc.nii.gz
Update not needed
-rw-rw-r-- 1 tapsya jackbgp 246609172 Aug 8 23:12 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/005/fmc.siemens.nii.gz
-rw-rw-r-- 1 tapsya jackbgp 237855956 Aug 8 22:09 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/005/fmc.nii.gz
Update not needed
-rw-rw-r-- 1 tapsya jackbgp 248572028 Aug 8 23:18 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/009/fmc.siemens.nii.gz
-rw-rw-r-- 1 tapsya jackbgp 242048296 Aug 8 22:12 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/009/fmc.nii.gz
Update not needed
-rw-rw-r-- 1 tapsya jackbgp 648926421 Aug 8 23:46 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/010/fmc.siemens.nii.gz
-rw-rw-r-- 1 tapsya jackbgp 628947011 Aug 8 22:19 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/010/fmc.nii.gz
Update not needed
-rw-rw-r-- 1 tapsya jackbgp 406063516 Aug 8 23:59 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/011/fmc.siemens.nii.gz
-rw-rw-r-- 1 tapsya jackbgp 390877351 Aug 8 22:26 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/011/fmc.nii.gz
Update not needed
Started at Wed Aug 10 14:46:57 EDT 2011
Ended at Wed Aug 10 14:46:58 EDT 2011
stc-sess Done
avml07 Volume Smoothing ---------------------
spatialsmooth-sess -i fmc.siemens -o fmc.siemens.sm6 -fwhm 6 -fsd bold -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -rlf runlist -nolog -update
------------------------------------------------
------------------------------------------------
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07
Wed Aug 10 14:46:59 EDT 2011
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold /space/adapt/1/users/tapsya/project_AVISI
RunList 002 003 005 009 010 011
-------------------------------------------------
1/1 avml07 1/6 002 Wed Aug 10 14:46:59 EDT 2011
avml07 002 Update not needed
-------------------------------------------------
1/1 avml07 2/6 003 Wed Aug 10 14:47:00 EDT 2011
avml07 003 Update not needed
-------------------------------------------------
1/1 avml07 3/6 005 Wed Aug 10 14:47:00 EDT 2011
avml07 005 Update not needed
-------------------------------------------------
1/1 avml07 4/6 009 Wed Aug 10 14:47:00 EDT 2011
avml07 009 Update not needed
-------------------------------------------------
1/1 avml07 5/6 010 Wed Aug 10 14:47:00 EDT 2011
avml07 010 Update not needed
-------------------------------------------------
1/1 avml07 6/6 011 Wed Aug 10 14:47:01 EDT 2011
avml07 011 Update not needed
Started at Wed Aug 10 14:46:59 EDT 2011
Ended at Wed Aug 10 14:47:01 EDT 2011
spatiallysmooth-sess Done
----------------------------------------
Started at Wed Aug 10 14:46:44 EDT 2011
Ended at Wed Aug 10 14:47:01 EDT 2011
preproc-sess done
-------------------------------------------
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07
Wed Aug 10 14:47:05 EDT 2011
anadir = /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/FIRsm6pf2.vol
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
MNE_ROOT was not set. MNE Matlab tools will not accessible
>> >> >> >> >> >> >> /usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# avml07 ###############################
/autofs/space/adapt_001/users/tapsya/project_AVISI/avml07
-------------------------
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/stable5_1_0/matlab/MRIread.m
-------------------------
outtop = /autofs/space/adapt_001/users/tapsya/project_AVISI
Extension format = nii.gz
1 A1-REST.mat
2 A2-REST.mat
3 A4-REST.mat
4 AT1-REST.mat
5 AT2-REST.mat
6 AT4-REST.mat
7 AV1-REST.mat
8 AV2-REST.mat
9 AV4-REST.mat
10 AVT1-REST.mat
11 AVT2-REST.mat
12 AVT4-REST.mat
13 IAV1.mat
14 IAV2.mat
15 IAV4.mat
16 V1-REST.mat
17 V2-REST.mat
18 V4-REST.mat
19 VT1-REST.mat
20 VT2-REST.mat
21 VT4-REST.mat
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
nruns = 6
autostimdur =
outanadir = /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/FIRsm6pf2.vol
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Ignoring stimulus duration for FIR model
Excluding 3 points
Found 44425/102400 (43.4) voxels in mask
Creating Design Matrix
... creation time = 0.124 sec
DoMCFit = 1
ntptot = 7004, nX = 342, DOF = 6662
Saving X matrix to /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07/bold/FIRsm6pf2.vol/Xtmp.mat
XCond = 1925.74 (normalized)
Computing compensation for resdual AR1 bias
1 -0.5 -0.47706 (t=596.457)
2 -0.25 -0.240053 (t=1015.5)
3 0 -0.00372243 (t=1147.08)
4 0.25 0.231421 (t=1564.53)
5 0.5 0.463763 (t=2153.58)
AR1 Correction M: 0.00545044 1.0624
Computing contrast matrices
OLS Beta Pass
run 1 t= 0.2
Global Mean 378.05
run 2 t=34.6
Global Mean 375.24
run 3 t=85.4
Global Mean 370.98
run 4 t=108.3
Global Mean 364.14
run 5 t=130.3
Global Mean 367.05
run 6 t=180.1
Global Mean 366.68
Global In-Mask Mean = 370.355 (260.414)
Rescale Target = 100
RescaleFactor = 0.270011
OLS Residual Pass
run 1 t= 0.0
??? Error using ==> unknown
Out of memory. Type HELP MEMORY for your options.
Error in ==> fast_selxavg3 at 469
rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun;
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n_______________________________________________
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