Hi,
I know that mri_glmfit and mri_surfcluster can be used to threshold activity on the surface using a monte carlo simulation, but I was wondering if it is possible to do this on data that has been constrained by an anatomical label.
I think this could be described as the Monte Carlo analog of tksurfer's FDR "marked label only" option.
The documentation lists 3 steps for the more general case:
1.
Estimation: run the analysis on your data without simulation. Note: at this point you can view your results with FDR thresholding in tksurfer. FDR is often conservative relative to cluster-based thresholding.
2.
Simulation: run the simulator with the same parameters as the estimation to get the Cluster Simulation Data (CSD).
3.
Clustering: run mri_surfcluster, passing it the CSD from the simulator and the output of the estimation. These programs will print out clusters along with their p-values.
Where in this flow, and how, could func2roi be used to limit everything to activity taking place in an ROI?
I have a guess, but I think it is at best overcomplicated and worst not possible to do (this way).
1. Run mkcontrast and stxgrinder to generate the significance maps for the contrasts, given the list of subjects. 2. Using mris_preproc, resample the data onto average7 This generates mgh files. 3. Run func2roi to constrain the contrasts, for subject average7, using the ROI labels. I'm not so sure about this step. Can this input be specified to func2roi? Is it possible to do this? The output side of this step is a little more clear than the input. One of the ouputs of func2roi are bfloat files. bfloat: "This is where the hemodynamic averages (as computed by selxavg-sess) averaged within the ROI are stored." 4. Using mri_surf2surf, convert the bfloat files to mgh files.
5. Create a group descriptor file to compare between groups. Is this done manually, or using a specific program? 6. Run mri_glmfit on the mgh files to estimate at a predefined significance level. 7. Run mri_glmfit again on the same files to simulate random null hypothesis data. 8. Run mri_surfcluster to generate clusters at a p-value based on a monte carlo algorithm using the null data vs. 'real' hypothesis data.
Thanks in advance, Rob
Actually, you don't use func2roi, just specify the label with --label in mri_glmfit, and I think you're good to go. If you're going to use the monte carlo simulation, make sure you specify the approriate fwhm to mri_glmfit when doing the simulation (regardless of the value you used when running it in step 1).
doug
On Fri, 29 Jun 2007, Robert Levy wrote:
Hi,
I know that mri_glmfit and mri_surfcluster can be used to threshold activity on the surface using a monte carlo simulation, but I was wondering if it is possible to do this on data that has been constrained by an anatomical label. I think this could be described as the Monte Carlo analog of tksurfer's FDR "marked label only" option.
The documentation lists 3 steps for the more general case:
Estimation: run the analysis on your data without simulation. Note: at this point you can view your results with FDR thresholding in tksurfer. FDR is often conservative relative to cluster-based thresholding.
Simulation: run the simulator with the same parameters as the estimation to get the Cluster Simulation Data (CSD).
Clustering: run mri_surfcluster, passing it the CSD from the simulator and the output of the estimation. These programs will print out clusters along with their p-values.
Where in this flow, and how, could func2roi be used to limit everything to activity taking place in an ROI? I have a guess, but I think it is at best overcomplicated and worst not possible to do (this way).
- Run mkcontrast and stxgrinder to generate the significance maps for the
contrasts, given the list of subjects. 2. Using mris_preproc, resample the data onto average7 This generates mgh files. 3. Run func2roi to constrain the contrasts, for subject average7, using the ROI labels. I'm not so sure about this step. Can this input be specified to func2roi? Is it possible to do this? The output side of this step is a little more clear than the input. One of the ouputs of func2roi are bfloat files. bfloat: "This is where the hemodynamic averages (as computed by selxavg-sess) averaged within the ROI are stored." 4. Using mri_surf2surf, convert the bfloat files to mgh files. 5. Create a group descriptor file to compare between groups. Is this done manually, or using a specific program? 6. Run mri_glmfit on the mgh files to estimate at a predefined significance level. 7. Run mri_glmfit again on the same files to simulate random null hypothesis data. 8. Run mri_surfcluster to generate clusters at a p-value based on a monte carlo algorithm using the null data vs. 'real' hypothesis data.
Thanks in advance, Rob
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)
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There is a sig.nii there. Is that not what you want? Also, you should use fsaverage as the target. we're trying to depricate average7
doug
Robert Levy wrote:
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, my mistake, I'm still a newbie to Freesurfer, and I was confused about what files it was supposed to create. The mris_preproc in /space/greve/... worked. Thanks, Rob
Doug Greve wrote:
There is a sig.nii there. Is that not what you want? Also, you should use fsaverage as the target. we're trying to depricate average7 1
doug
Robert Levy wrote:
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Rob,
Trying setting the env variables like this if you are in dev env and want the bhdr files. setenv FSF_OUTPUT_FORMAT bhdr
Doug is replacing all the fsfast output formats to be in .nii
Balaji
Robert Levy wrote:
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Balaji Lakshmanan -
Doug Greve -
Robert Levy