Hi Doug,
Thanks for getting back to me. I tried deleting those files, and got the same
error, although the terminal output looked slightly different towards the end
(in terms of the compensation values).
Here it is below:
--------------------------------------------------------------
selxavg3-sess logfile is
/autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log
--------------------------------------------------------------
preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_050514 -nolog
--------------------------------------------------------------
preproc-sess logfile is /dev/null
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
arodthom
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
/autofs/cluster/roffman/users/Stable5_PerRun
/usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess
-s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a
SIRP_LoadRegression_Stable5_050514 -nolog
Tue Aug 4 12:12:17 EDT 2015
instem f
mc 1 f fmcpr
stc 0 fmcpr
sm 0 fmcpr
mask 1 brain
GDDA098 Template -----------------------------
mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd
bold -rlf runlistfile -nolog -update
Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 ----------------
Tue Aug 4 12:12:17 EDT 2015
Detected input format at nii
GDDA098 Update not needed
Run: 015 ----------------
Tue Aug 4 12:12:17 EDT 2015
GDDA098 015 Update not needed
Run: 016 ----------------
Tue Aug 4 12:12:17 EDT 2015
GDDA098 016 Update not needed
Run: 017 ----------------
Tue Aug 4 12:12:17 EDT 2015
GDDA098 017 Update not needed
Tue Aug 4 12:12:17 EDT 2015
mktemplate-sess completed
GDDA098 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d
/autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update
------------------------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
Tue Aug 4 12:12:17 EDT 2015
WARNING: multiple formats found for template
USING: template.nii.gz
GDDA098 Update not needed for session-level mask
WARNING: multiple formats found for 015/template
USING: 015/template.nii.gz
GDDA098 Update not needed for run 015 mask
GDDA098 Update not needed for run 015 meanval
WARNING: multiple formats found for 016/template
USING: 016/template.nii.gz
GDDA098 Update not needed for run 016 mask
GDDA098 Update not needed for run 016 meanval
WARNING: multiple formats found for 017/template
USING: 017/template.nii.gz
GDDA098 Update not needed for run 017 mask
GDDA098 Update not needed for run 017 meanval
Tue Aug 4 12:12:18 EDT 2015
mkbrainmask-sess done
GDDA098 Registration -----------------------------
register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd
bold -dof 6 -rlf runlistfile -per-run -nolog -update
--------------------------------------------------------------
register-sess logfile is /dev/null
--------------------------------------------------------------
Tue Aug 4 12:12:18 EDT 2015
setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
cd /autofs/cluster/roffman/users/Stable5_PerRun
/usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d
/autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile
-per-run -nolog -update
cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or
directory
Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 ----------------
Tue Aug 4 12:12:18 EDT 2015
Run: 015 ----------------
Tue Aug 4 12:12:18 EDT 2015
WARNING: multiple formats found for bold/015/template
USING: bold/015/template.nii.gz
Update not needed
Run: 016 ----------------
Tue Aug 4 12:12:18 EDT 2015
WARNING: multiple formats found for bold/016/template
USING: bold/016/template.nii.gz
Update not needed
Run: 017 ----------------
Tue Aug 4 12:12:18 EDT 2015
WARNING: multiple formats found for bold/017/template
USING: bold/017/template.nii.gz
Update not needed
Tue Aug 4 12:12:18 EDT 2015
register-sess completed
GDDA098 MC -----------------------------
mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -d
/autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile
-per-run -nolog -update
Logfile is /dev/null
-------------------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
RunList: 015 016 017
WARNING: multiple formats found for 015/template
USING: 015/template.nii.gz
GDDA098 015 Update not needed
WARNING: multiple formats found for 016/template
USING: 016/template.nii.gz
GDDA098 016 Update not needed
WARNING: multiple formats found for 017/template
USING: 017/template.nii.gz
GDDA098 017 Update not needed
Tue Aug 4 12:12:18 EDT 2015
mc-sess completed SUCCESSFULLY
----------------------------------------
Started at Tue Aug 4 12:12:17 EDT 2015
Ended at Tue Aug 4 12:12:18 EDT 2015
preproc-sess done
-------------------------------------------
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
Tue Aug 4 12:12:19 EDT 2015
anadir =
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------
No window system found. Java option 'MWT' ignored.
Warning: Unable to open display 'iconic'. You will not be able to display
graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored.
< M A T L A B (R) >
Copyright 1984-2013 The MathWorks, Inc.
R2013b (8.2.0.701) 64-bit (glnxa64)
August 13, 2013
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
>> >> >> >> >> >> >>
sxa3pwd =
/autofs/cluster/roffman/users/Stable5_PerRun
>>
sxa3cmd =
/usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -s GDDA098 -analysis
SIRP_LoadRegression_Stable5_050514
>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# GDDA098 ###############################
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
-------------------------
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/stable5_3_0/matlab/MRIread.m
-------------------------
outtop = /autofs/cluster/roffman/users/Stable5_PerRun
Extension format = nii.gz
1 Cond2vFix.mat
Excluding 0 points
nruns = 3
autostimdur =
outanadir =
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514
Excluding 0 points
Excluding 0 points
Excluding 0 points
Found 49193/143360 (34.3) voxels in mask
Creating Design Matrix
... creation time = 0.011 sec
DoMCFit = 1
ntptot = 705, nX = 18, DOF = 687
Saving X matrix to
/autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514/Xtmp.mat
XCond = 35.9364 (normalized)
Computing compensation for resdual AR1 bias
1 -0.5 -0.507451 (t=0.046548)
2 -0.25 -0.264 (t=0.105696)
3 0 -0.0235997 (t=0.137308)
4 0.25 0.211292 (t=0.189719)
5 0.5 0.434363 (t=0.217673)
AR1 Correction M: 0.031657 1.0595
Computing contrast matrices
OLS Beta Pass
run 1 t= 0.0
ERROR: dimension mismatch between mask and 1th run
>> ------------------------------------------
ERROR: fast_selxavg3() failed\n
________________________________________
From: [email protected]
[[email protected]] on behalf of Douglas N Greve
[[email protected]]
Sent: Tuesday, August 04, 2015 11:39 AM
To: [email protected]
Subject: Re: [Freesurfer] Dimension mismatch between mask and run
I'm not sure, but it may be that there are some files that are nii and
others that are nii.gz. Eg,
ls -tl /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/015/masks/
total 1248
-rw-rw---- 1 arodthom roffmagp 3579 Aug 3 18:06 brain.e3.nii.gz
-rw-rw---- 1 arodthom roffmagp 5383 Aug 3 18:06 brain.nii.gz
-rw-rw---- 1 arodthom roffmagp 606560 Mar 16 11:02 brain.e3.nii
-rw-rw---- 1 arodthom roffmagp 606560 Mar 16 11:02 brain.nii
The nii.gz are newer but I think selxavg3-sess will use the nii files,
which have probably not been updated. Try deleting the same-named nii files
On 08/03/2015 06:32 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> For a data set of n=100, selxavg3 is erroring out on 10 subjects (GDDA086,
> 88, 89, 91, 93, 94, 95, 96, 97, and 98). It says ERROR: dimension mismatch
> between mask and 1th run. Do you know why freesurfer is having trouble with
> these subjects in particular, and how I can avoid this error?
>
> Thanks for your help,
> Anais
>
> Below is the terminal window output:
> --------------------------------------------------------------
> selxavg3-sess logfile is
> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150803173934.log
> --------------------------------------------------------------
> preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a
> SIRP_LoadRegression_Stable5_050514 -nolog
> --------------------------------------------------------------
> preproc-sess logfile is /dev/null
> --------------------------------------------------------------
> $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> arodthom
> setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
> setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
> Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014
> x86_64 x86_64 x86_64 GNU/Linux
> /autofs/cluster/roffman/users/Stable5_PerRun
> /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess
> -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a
> SIRP_LoadRegression_Stable5_050514 -nolog
> Mon Aug 3 17:39:35 EDT 2015
> instem f
> mc 1 f fmcpr
> stc 0 fmcpr
> sm 0 fmcpr
> mask 1 brain
> GDDA098 Template -----------------------------
> mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun
> -fsd bold -rlf runlistfile -nolog -update
>
> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 ----------------
> Mon Aug 3 17:39:36 EDT 2015
> Detected input format at nii
> GDDA098 Update not needed
> Run: 015 ----------------
> Mon Aug 3 17:39:36 EDT 2015
> GDDA098 015 Update not needed
> Run: 016 ----------------
> Mon Aug 3 17:39:36 EDT 2015
> GDDA098 016 Update not needed
> Run: 017 ----------------
> Mon Aug 3 17:39:36 EDT 2015
> GDDA098 017 Update not needed
> Mon Aug 3 17:39:36 EDT 2015
> mktemplate-sess completed
> GDDA098 Mask ------------------------
> mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d
> /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update
> ------------------------------------------------
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
> Mon Aug 3 17:39:36 EDT 2015
> WARNING: multiple formats found for template
> USING: template.nii.gz
> GDDA098 Update not needed for session-level mask
> WARNING: multiple formats found for 015/template
> USING: 015/template.nii.gz
> GDDA098 Update not needed for run 015 mask
> GDDA098 Update not needed for run 015 meanval
> WARNING: multiple formats found for 016/template
> USING: 016/template.nii.gz
> GDDA098 Update not needed for run 016 mask
> GDDA098 Update not needed for run 016 meanval
> WARNING: multiple formats found for 017/template
> USING: 017/template.nii.gz
> GDDA098 Update not needed for run 017 mask
> GDDA098 Update not needed for run 017 meanval
> Mon Aug 3 17:39:37 EDT 2015
> mkbrainmask-sess done
> GDDA098 Registration -----------------------------
> register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd
> bold -dof 6 -rlf runlistfile -per-run -nolog -update
> --------------------------------------------------------------
> register-sess logfile is /dev/null
> --------------------------------------------------------------
> Mon Aug 3 17:39:37 EDT 2015
>
> setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun
> cd /autofs/cluster/roffman/users/Stable5_PerRun
> /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d
> /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf
> runlistfile -per-run -nolog -update
>
> cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or
> directory
> Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014
> x86_64 x86_64 x86_64 GNU/Linux
>
> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 ----------------
> Mon Aug 3 17:39:37 EDT 2015
> Run: 015 ----------------
> Mon Aug 3 17:39:37 EDT 2015
> WARNING: multiple formats found for bold/015/template
> USING: bold/015/template.nii.gz
> Update not needed
> Run: 016 ----------------
> Mon Aug 3 17:39:37 EDT 2015
> WARNING: multiple formats found for bold/016/template
> USING: bold/016/template.nii.gz
> Update not needed
> Run: 017 ----------------
> Mon Aug 3 17:39:37 EDT 2015
> WARNING: multiple formats found for bold/017/template
> USING: bold/017/template.nii.gz
> Update not needed
> Mon Aug 3 17:39:37 EDT 2015
> register-sess completed
> GDDA098 MC -----------------------------
> mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -d
> /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile
> -per-run -nolog -update
> Logfile is /dev/null
> -------------------------------------------
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
> RunList: 015 016 017
> WARNING: multiple formats found for 015/template
> USING: 015/template.nii.gz
> GDDA098 015 Update not needed
> WARNING: multiple formats found for 016/template
> USING: 016/template.nii.gz
> GDDA098 016 Update not needed
> WARNING: multiple formats found for 017/template
> USING: 017/template.nii.gz
> GDDA098 017 Update not needed
>
>
> Mon Aug 3 17:39:38 EDT 2015
> mc-sess completed SUCCESSFULLY
> ----------------------------------------
> Started at Mon Aug 3 17:39:35 EDT 2015
> Ended at Mon Aug 3 17:39:38 EDT 2015
> preproc-sess done
> -------------------------------------------
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
> Mon Aug 3 17:39:38 EDT 2015
> anadir =
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514
> DoGLMFit = 1
> DoContrasts = 1
> UpdateNeeded = 1
> ------------------------------------------
> ------- matlab output --------------------
> Warning: Unable to open display 'iconic'. You will not be able to display
> graphics on the screen.
> Warning: No window system found. Java option 'MWT' ignored.
>
> < M A T L A B (R) >
> Copyright 1984-2013 The MathWorks, Inc.
> R2013b (8.2.0.701) 64-bit (glnxa64)
> August 13, 2013
>
> No window system found. Java option 'MWT' ignored.
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
>
> sxa3pwd =
>
> /autofs/cluster/roffman/users/Stable5_PerRun
>
> sxa3cmd =
>
> /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -s GDDA098
> -analysis SIRP_LoadRegression_Stable5_050514
>
>>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m
> #@# GDDA098 ###############################
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
> -------------------------
> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m
> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_ldanaflac.m
> /usr/local/freesurfer/stable5_3_0/matlab/MRIread.m
> -------------------------
> outtop = /autofs/cluster/roffman/users/Stable5_PerRun
> Extension format = nii.gz
> 1 Cond2vFix.mat
> Excluding 0 points
> nruns = 3
> autostimdur =
>
>
> outanadir =
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514
> Excluding 0 points
> Excluding 0 points
> Excluding 0 points
> Found 49193/143360 (34.3) voxels in mask
> Creating Design Matrix
> ... creation time = 0.011 sec
> DoMCFit = 1
> ntptot = 705, nX = 18, DOF = 687
> Saving X matrix to
> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514/Xtmp.mat
> XCond = 35.9364 (normalized)
> Computing compensation for resdual AR1 bias
> 1 -0.5 -0.507451 (t=0.033876)
> 2 -0.25 -0.264 (t=0.081305)
> 3 0 -0.0235997 (t=0.100205)
> 4 0.25 0.211292 (t=0.143646)
> 5 0.5 0.434363 (t=0.160328)
> AR1 Correction M: 0.031657 1.0595
> Computing contrast matrices
> OLS Beta Pass
> run 1 t= 0.4
> ERROR: dimension mismatch between mask and 1th run
>>> ------------------------------------------
> ERROR: fast_selxavg3() failed\n
>
> _______________________________________________
> Freesurfer mailing list
> [email protected]
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[email protected]
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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