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
[levy@vantz SUBJECTS_DIR]$ pwd /space/ventzl/1/users/SUBJECTS_DIR [levy@vantz 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)