Hello,
Thanks for the solution to the mkcontrast-sess problem.
I thought that re-running stxgrinder would solve another problem I'm
having, trying to run mris_preproc, but it didn't seem to be the
answer. However I still think it is because something is amiss with
mk-contrast/stxgrinder that I'm having this problem. These are the only
files that stxgrinder generated (in a subject's directory for that
contrast).
ASvfix_6.mat ces.nii cespct.nii cesvar.nii f.nii fsig.nii sig.nii
t.nii
I included the environment/command/resulting error below for mkcontrast
and stxgrinder below
When I try to run mris_preproc, it of course fails because ces.bhdr is
missing. Also, the file exists for contrasts that were run in the
past. Does stx_grinder create that file, or does some other process
generate it? Are there any reasons why stx_grinder might not generate
that file (assuming it should)?
I know that at least one thing is wrong, either in my command-line
parameters, or somewhere in the code, because stxgrinder didn't make any
sig files.
Thanks,
Rob
[EMAIL PROTECTED] SUBJECTS_DIR]$ pwd
/space/ventzl/1/users/SUBJECTS_DIR
[EMAIL PROTECTED] SUBJECTS_DIR]$ use_dev
-------- freesurfer-Linux-centos4_x86_64-dev-20070703 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/dev
FSFAST_HOME /usr/local/freesurfer/dev/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR
MNI_DIR /usr/local/freesurfer/dev/mni
FSL_DIR /usr/local/freesurfer/dev/fsl
[vantz:SUBJECTS_DIR] (nmr-dev-env) mkcontrast-sess -analysis EMerror
-contrast ASvfix_6 -a 2 -c 0 -setwdelay -sumdelays
INFO: Found 12 Delays
INFO: Found 4 Non-Null Conditions
Condition Weights: 0 1.00000000000000000000 0 0
###################################
### Enter 12 Delay Weights (Return)
0 0 0 0 0 0 1 0 0 0 0 0
mkcontrast -anadir EMerror -wcond 0 1.00000000000000000000 0 0 -sumconds
-o EMer ror/ASvfix_6 -sumdelays -wdelay 0 0 0 0 0 0 1 0 0 0 0 0 -setwdelay
$Id: mkcontrast,v 1.7 2007/06/13 01:02:48 greve Exp $
cmtxfile EMerror/ASvfix_6
nconds 4, wcond 0 1.00000000000000000000 0 0
ndelays 12, wdelay 0 0 0 0 0 0 1 0 0 0 0 0
ndelays 12, wpsa
sumconds 1
sumdelays 1
nircorr 0
TER 2
rdelta
rtau
Warning: Unable to open display iconic, MATLAB is starting without a
display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
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
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> >> >> >> Normalizing contrast matrix
>> >> >> >> >> >> >> >> Tue Jul 3 14:14:42 EDT 2007
[vantz:SUBJECTS_DIR] (nmr-dev-env) stxgrinder-sess -a EMerror -c
ASvfix_6 -sf Subject_Lists/bw-group-error-5
--------------------------------------------------------------
stxgrinder-sess logfile is
/autofs/space/ventzl_001/users/SUBJECTS_DIR/log/stxgrinder-sess.070703141530.log
--------------------------------------------------------------
Contrast List: ASvfix_6
MLF is /tmp/stxgrinder-sess-19476.m
-----------------------------------------------------
Warning: Unable to open display iconic, MATLAB is starting without a
display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
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/dev/fsfast/toolbox/fast_stxgrinder2_sess.m
>>
UseMRIread = 1, ext = nii
nthsess = 1 mano001 time=0.014987 --------
/autofs/space/ventzl_006/users/EMexec/fMRI/mano001
contrast ASvfix_6 (time=1.06361)
VRF: 33.756
slice 0 Warning: Function call tTest invokes
/usr/local/freesurfer/dev/fsfast/toolbox/tTest.m,
however, function /usr/pubsw/common/matlab/7.1/toolbox/stats/ttest.m
that differs only in case precedes it on the path.
> In fast_stxgrinder2_sess at 241
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 2 mano002 time=8.06025 --------
/autofs/space/balagula_006/users/EMexec/fMRI/mano002
contrast ASvfix_6 (time=8.10209)
VRF: 30.5989
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 3 mano004 time=13.918 --------
/autofs/space/balagula_006/users/EMexec/fMRI/mano004
contrast ASvfix_6 (time=13.9526)
VRF: 34.1394
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 4 mano005 time=19.8164 --------
/autofs/space/balagula_002/users/EMexec/fMRI/mano005
contrast ASvfix_6 (time=19.8518)
VRF: 35.8863
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 5 mano007 time=25.6837 --------
/autofs/space/balagula_002/users/EMexec/fMRI/mano007
contrast ASvfix_6 (time=25.7182)
VRF: 35.3363
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 6 mano008 time=31.6722 --------
/autofs/space/balagula_002/users/EMexec/fMRI/mano008
contrast ASvfix_6 (time=31.7073)
VRF: 25.6896
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 7 mano009 time=37.4948 --------
/autofs/space/balagula_002/users/EMexec/fMRI/mano009
contrast ASvfix_6 (time=37.5298)
VRF: 41.6065
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 8 mano010 time=43.3794 --------
/autofs/space/balagula_007/users/EMexec/fMRI/mano010
contrast ASvfix_6 (time=43.415)
VRF: 27.7303
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 9 mano011 time=49.2284 --------
/autofs/space/balagula_004/users/EMexec/fMRI/mano011
contrast ASvfix_6 (time=49.2639)
VRF: 35.8992
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 10 mano012 time=55.0716 --------
/autofs/space/balagula_004/users/EMexec/fMRI/mano012
contrast ASvfix_6 (time=55.1065)
VRF: 32.94
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 11 mano013 time=61.2302 --------
/autofs/space/balagula_003/users/EMexec/fMRI/mano013
contrast ASvfix_6 (time=61.2789)
VRF: 36.1235
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 12 mano014 time=67.1996 --------
/autofs/space/balagula_003/users/EMexec/fMRI/mano014
contrast ASvfix_6 (time=67.2352)
VRF: 36.6775
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 13 mano016 time=73.0689 --------
/autofs/space/balagula_007/users/EMexec/fMRI/mano016
contrast ASvfix_6 (time=73.1052)
VRF: 81.0005
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 14 mano025 time=79.4791 --------
/autofs/space/balagula_004/users/EMexec/fMRI/mano025
contrast ASvfix_6 (time=79.5151)
VRF: 31.7935
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 15 manoA02 time=85.3484 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA02
contrast ASvfix_6 (time=85.3841)
VRF: 29.5667
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 16 manoA03 time=91.4144 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA03
contrast ASvfix_6 (time=91.4503)
VRF: 32.5825
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 17 manoA04 time=97.2672 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA04
contrast ASvfix_6 (time=97.303)
VRF: 29.7342
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 18 manoA05 time=103.239 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA05
contrast ASvfix_6 (time=103.275)
VRF: 27.022
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 19 manoA07 time=109.276 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA07
contrast ASvfix_6 (time=109.311)
VRF: 33.9482
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 20 manoA08 time=115.161 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA08
contrast ASvfix_6 (time=115.196)
VRF: 32.6989
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 21 manoA09 time=121.121 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA09
contrast ASvfix_6 (time=121.157)
VRF: 28.419
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 22 manoA10 time=127.045 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA10
contrast ASvfix_6 (time=127.081)
VRF: 31.6634
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 23 manoA11 time=132.884 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA11
contrast ASvfix_6 (time=132.92)
VRF: 35.0311
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
nthsess = 24 manoA13 time=138.957 --------
/autofs/space/balagula_007/users/EMexec/fMRI/manoA13
contrast ASvfix_6 (time=138.993)
VRF: 35.6392
slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
done 144.807
>> >>
Started at Tue Jul 3 14:15:31 EDT 2007
Ended at Tue Jul 3 14:17:59 EDT 2007
stxgrinder-sess completed
[vantz:SUBJECTS_DIR] (nmr-dev-env) mris_preproc --fsgd
fsgd_and_contrast_files/BwGroupError5.fsgd --target average7 --hemi lh
--sf Subject_Lists/bw-group-error-5 --a EMerror --c ASvfix_6 --out
lh.ASvfix_8s_BwGroupError5.fsfast.mgh
ERROR: cannot find
/autofs/space/ventzl_006/users/EMexec/fMRI/mano001/bold/EMerror/ASvfix_6/ces.bhdr
[vantz:SUBJECTS_DIR] (nmr-dev-env)
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
