Hi Doug,
Thanks again. I think something must be wrong with stxgrinder though as well, because no sig files were generated. Do you know what might have gone wrong there (I included the output of mkcontrast/stxgrinder in the previous email just in case you need to see that in order trace the source of the problem).
Thanks, Rob
Doug Greve wrote:
ok, this should be fixed too at the next dev update. Or you can use the version in:
/space/greve/1/users/greve/freesurfer/bin/mris_preproc
This version will not be stable long-term, so only use it until dev gets updated.
doug
Robert Levy wrote:
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, 2005To 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, 2005To 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)
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