Hi,
I am having problem when running the Monte Carlo script. The script seems to fail after only a few simulations but it does not give me any error message, it just says 'killed'. I am running it on 126 participants (2 groups of 63) and I have tried it on a number of different measures (sulc, area etc.). I thought it may be an space issue but I cleared all other files but that did not seem to make any difference.
This is what is printed out on the terminal:
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwritecmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 --surf fsaverage rh --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat WARNING: unrecognized mri_glmfit cmd option dods SURFACE: fsaverage rh /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim--glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite$Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $Thu Apr 24 18:58:31 IST 2014Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linuxfitzgejesetenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0DoPoll = 0DoPBSubmit = 0DoBackground = 0DiagCluster = 0gd2mtx = dodsfwhm = 21.770250nSimPerJob = 100001/1 Thu Apr 24 18:58:31 IST 2014mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh whiteINFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed reading group avg surface area 822 cm^2 from fileReading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mghreading group avg surface area 822 cm^2 from fileReading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mghsimbase Rh_JacobianW_15/csd/mc-z.negative.j001gdfReadHeader: reading Rh_JacobianW_15/y.fsgdINFO: demeaning continous variablesContinuous Variable Means (all subjects)Class Means of each Continuous Variable1 groupASD2 groupCTRLINFO: gd2mtx_method is dodsReading source surface /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.whiteNumber of vertices 163842Number of faces 327680Total area 65020.765625AvgVtxArea 0.396850AvgVtxDist 0.717994StdVtxDist 0.193566INFO: fwhm2niters: NOT fixing group surface areaSurface smoothing by fwhm=21.770250, niters=441.000000 $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $cwd /projects/pi-lgallagh/HPC_12_00408/qdeccmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white sysname Linuxhostname lonsdale01.clustermachine x86_64user fitzgejeFixVertexAreaFlag = 1UseMaskWithSmoothing 1fwhm 21.770250niters 441.000000OneSampleGroupMean 0y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mghlogyflag 0usedti 0FSGD Rh_JacobianW_15/y.fsgdlabelmask /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.labelmask Rh_JacobianW_15/mask.mghmaskinv 0glmdir (null)IllCondOK 0DoFFx 0Loading y from /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mghINFO: gd2mtx_method is dodsMatrix condition is 1/projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.labelFound 149926 points in label.Found 149926 voxels in masksearch space = 75188.6DOF = 124thresh = 1.3, threshadj = 0.99897
Starting simulation sim over 10000 trialsSmoothing done, nsteps = 441, tsec = 69.733Smoothing done, nsteps = 441, tsec = 69.799Smoothing done, nsteps = 441, tsec = 69.754Smoothing done, nsteps = 441, tsec = 69.749Smoothing done, nsteps = 441, tsec = 69.743Smoothing done, nsteps = 441, tsec = 69.749Smoothing done, nsteps = 441, tsec = 69.737Smoothing done, nsteps = 441, tsec = 69.738Smoothing done, nsteps = 441, tsec = 69.734Smoothing done, nsteps = 441, tsec = 69.806Smoothing done, nsteps = 441, tsec = 70.012Smoothing done, nsteps = 441, tsec = 70.139
Killed
Any suggestions that may help?
Kind regards,
Jackie
First of all, do you really need to run the simulation? If you are just doing a whole hemisphere analysis on fsaverage, then you can use the precomputed option.
doug
On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote:
Hi,
I am having problem when running the Monte Carlo script. The script seems to fail after only a few simulations but it does not give me any error message, it just says 'killed'. I am running it on 126 participants (2 groups of 63) and I have tried it on a number of different measures (sulc, area etc.). I thought it may be an space issue but I cleared all other files but that did not seem to make any difference.
This is what is printed out on the terminal:
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite
cmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 --surf fsaverage rh --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat
WARNING: unrecognized mri_glmfit cmd option dods
SURFACE: fsaverage rh
/home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim
--glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite
$Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $
Thu Apr 24 18:58:31 IST 2014
Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
fitzgeje
setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/
FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 21.770250
nSimPerJob = 10000
1/1 Thu Apr 24 18:58:31 IST 2014
mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
reading group avg surface area 822 cm^2 from file
Reading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
reading group avg surface area 822 cm^2 from file
Reading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
simbase Rh_JacobianW_15/csd/mc-z.negative.j001
gdfReadHeader: reading Rh_JacobianW_15/y.fsgd
INFO: demeaning continous variables
Continuous Variable Means (all subjects)
Class Means of each Continuous Variable
1 groupASD
2 groupCTRL
INFO: gd2mtx_method is dods
Reading source surface /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
INFO: fwhm2niters: NOT fixing group surface area
Surface smoothing by fwhm=21.770250, niters=441.000000
$Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
cwd /projects/pi-lgallagh/HPC_12_00408/qdec
cmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white
sysname Linux
hostname lonsdale01.cluster
machine x86_64
user fitzgeje
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
fwhm 21.770250
niters 441.000000
OneSampleGroupMean 0
y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh
logyflag 0
usedti 0
FSGD Rh_JacobianW_15/y.fsgd
labelmask /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
mask Rh_JacobianW_15/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
DoFFx 0
Loading y from /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh
INFO: gd2mtx_method is dods
Matrix condition is 1
/projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
Found 149926 points in label.
Found 149926 voxels in mask
search space = 75188.6
DOF = 124
thresh = 1.3, threshadj = 0.99897
Starting simulation sim over 10000 trials
Smoothing done, nsteps = 441, tsec = 69.733
Smoothing done, nsteps = 441, tsec = 69.799
Smoothing done, nsteps = 441, tsec = 69.754
Smoothing done, nsteps = 441, tsec = 69.749
Smoothing done, nsteps = 441, tsec = 69.743
Smoothing done, nsteps = 441, tsec = 69.749
Smoothing done, nsteps = 441, tsec = 69.737
Smoothing done, nsteps = 441, tsec = 69.738
Smoothing done, nsteps = 441, tsec = 69.734
Smoothing done, nsteps = 441, tsec = 69.806
Smoothing done, nsteps = 441, tsec = 70.012
Smoothing done, nsteps = 441, tsec = 70.139
Killed
Any suggestions that may help?
Kind regards,
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thank you for your reply. By precomputed do you mean the FDR in the GUI? Apologies I'm still new to the program!
I am planning on running an ROI analysis so will need to run it for that anyway (I think?)
Best,
Jackie
On 24 April 2014 21:47, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
First of all, do you really need to run the simulation? If you are just doing a whole hemisphere analysis on fsaverage, then you can use the precomputed option.
doug
On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote:
Hi,
I am having problem when running the Monte Carlo script. The script seems to fail after only a few simulations but it does not give me any error message, it just says 'killed'. I am running it on 126 participants (2 groups of 63) and I have tried it on a number of different measures (sulc, area etc.). I thought it may be an space issue but I cleared all other files but that did not seem to make any difference.
This is what is printed out on the terminal:
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite
cmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 --surf fsaverage rh --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C
/projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat
--C
/projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat
WARNING: unrecognized mri_glmfit cmd option dods
SURFACE: fsaverage rh
/home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim
--glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite
$Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $
Thu Apr 24 18:58:31 IST 2014
Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
fitzgeje
setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/
FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 21.770250
nSimPerJob = 10000
1/1 Thu Apr 24 18:58:31 IST 2014
mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C
Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
--C
Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
--mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
reading group avg surface area 822 cm^2 from file
Reading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
reading group avg surface area 822 cm^2 from file
Reading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
simbase Rh_JacobianW_15/csd/mc-z.negative.j001
gdfReadHeader: reading Rh_JacobianW_15/y.fsgd
INFO: demeaning continous variables
Continuous Variable Means (all subjects)
Class Means of each Continuous Variable
1 groupASD
2 groupCTRL
INFO: gd2mtx_method is dods
Reading source surface /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
INFO: fwhm2niters: NOT fixing group surface area
Surface smoothing by fwhm=21.770250, niters=441.000000
$Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
cwd /projects/pi-lgallagh/HPC_12_00408/qdec
cmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C
Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
--C
Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
--mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white
sysname Linux
hostname lonsdale01.cluster
machine x86_64
user fitzgeje
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
fwhm 21.770250
niters 441.000000
OneSampleGroupMean 0
y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh
logyflag 0
usedti 0
FSGD Rh_JacobianW_15/y.fsgd
labelmask /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
mask Rh_JacobianW_15/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
DoFFx 0
Loading y from /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh
INFO: gd2mtx_method is dods
Matrix condition is 1
/projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
Found 149926 points in label.
Found 149926 voxels in mask
search space = 75188.6
DOF = 124
thresh = 1.3, threshadj = 0.99897
Starting simulation sim over 10000 trials
Smoothing done, nsteps = 441, tsec = 69.733
Smoothing done, nsteps = 441, tsec = 69.799
Smoothing done, nsteps = 441, tsec = 69.754
Smoothing done, nsteps = 441, tsec = 69.749
Smoothing done, nsteps = 441, tsec = 69.743
Smoothing done, nsteps = 441, tsec = 69.749
Smoothing done, nsteps = 441, tsec = 69.737
Smoothing done, nsteps = 441, tsec = 69.738
Smoothing done, nsteps = 441, tsec = 69.734
Smoothing done, nsteps = 441, tsec = 69.806
Smoothing done, nsteps = 441, tsec = 70.012
Smoothing done, nsteps = 441, tsec = 70.139
Killed
Any suggestions that may help?
Kind regards,
Jackie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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No, I mean using the --cache option which will use precomputed tables rather than generating new ones
On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote:
Hi Doug,
Thank you for your reply. By precomputed do you mean the FDR in the GUI? Apologies I'm still new to the program!
I am planning on running an ROI analysis so will need to run it for that anyway (I think?)
Best,
Jackie
On 24 April 2014 21:47, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
First of all, do you really need to run the simulation? If you are just doing a whole hemisphere analysis on fsaverage, then you can use the precomputed option. doug On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > Hi, > > I am having problem when running the Monte Carlo script. The script > seems to fail after only a few simulations but it does not give me any > error message, it just says 'killed'. I am running it on 126 > participants (2 groups of 63) and I have tried it on a number of > different measures (sulc, area etc.). I thought it may be an space > issue but I cleared all other files but that did not seem to make any > difference. > > This is what is printed out on the terminal: > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 > --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite > > cmdline mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods > --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > --surf fsaverage rh --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat > --C > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat > > > > WARNING: unrecognized mri_glmfit cmd option dods > > > SURFACE: fsaverage rh > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign > neg --overwrite > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ > > Thu Apr 24 18:58:31 IST 2014 > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > fitzgeje > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > DoPoll = 0 > > DoPBSubmit = 0 > > DoBackground = 0 > > DiagCluster = 0 > > gd2mtx = dods > > fwhm = 21.770250 > > nSimPerJob = 10000 > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > --fsgd Rh_JacobianW_15/y.fsgd dods --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > --surf fsaverage rh white > > INFO: ignoring tag Creator > > INFO: ignoring tag SUBJECTS_DIR > > INFO: ignoring tag SynthSeed > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 groupASD > > 2 groupCTRL > > INFO: gd2mtx_method is dods > > Reading source surface > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65020.765625 > > AvgVtxArea 0.396850 > > AvgVtxDist 0.717994 > > StdVtxDist 0.193566 > > INFO: fwhm2niters: NOT fixing group surface area > > Surface smoothing by fwhm=21.770250, niters=441.000000 > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > cmdline mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > --fsgd Rh_JacobianW_15/y.fsgd dods --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > --surf fsaverage rh white > > sysname Linux > > hostname lonsdale01.cluster > > machine x86_64 > > user fitzgeje > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > fwhm 21.770250 > > niters 441.000000 > > OneSampleGroupMean 0 > > y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > logyflag 0 > > usedti 0 > > FSGD Rh_JacobianW_15/y.fsgd > > labelmask > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > mask Rh_JacobianW_15/mask.mgh > > maskinv 0 > > glmdir (null) > > IllCondOK 0 > > DoFFx 0 > > Loading y from > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > INFO: gd2mtx_method is dods > > Matrix condition is 1 > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > Found 149926 points in label. > > Found 149926 voxels in mask > > search space = 75188.6 > > DOF = 124 > > thresh = 1.3, threshadj = 0.99897 > > > > Starting simulation sim over 10000 trials > > Smoothing done, nsteps = 441, tsec = 69.733 > > Smoothing done, nsteps = 441, tsec = 69.799 > > Smoothing done, nsteps = 441, tsec = 69.754 > > Smoothing done, nsteps = 441, tsec = 69.749 > > Smoothing done, nsteps = 441, tsec = 69.743 > > Smoothing done, nsteps = 441, tsec = 69.749 > > Smoothing done, nsteps = 441, tsec = 69.737 > > Smoothing done, nsteps = 441, tsec = 69.738 > > Smoothing done, nsteps = 441, tsec = 69.734 > > Smoothing done, nsteps = 441, tsec = 69.806 > > Smoothing done, nsteps = 441, tsec = 70.012 > > Smoothing done, nsteps = 441, tsec = 70.139 > > > Killed > > > Any suggestions that may help? > > Kind regards, > > Jackie > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Jacqueline Fitzgerald PhD Candidate Department of Psychiatry / Trinity Institute of Neuroscience Room 3.36b Lloyd Building Trinity College Dublin Dublin 2
Tel: (01) 896 4102
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I had not realised that was possible, thanks for that. Will save alot of time! I am getting an error that the --cache flag is not recognised. This is the command I am running;
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15 --cache 2.3 neg --cwp 0.05 ERROR: Flag --cache unrecognized.
Is there an additional directory or step I need to do?
Thanks again for your help,
Best,
Jackie
On 28 April 2014 18:11, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
No, I mean using the --cache option which will use precomputed tables rather than generating new ones
On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote:
Hi Doug,
Thank you for your reply. By precomputed do you mean the FDR in the GUI? Apologies I'm still new to the program!
I am planning on running an ROI analysis so will need to run it for that anyway (I think?)
Best,
Jackie
On 24 April 2014 21:47, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
First of all, do you really need to run the simulation? If you are just doing a whole hemisphere analysis on fsaverage, then you can use the precomputed option. doug On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > Hi, > > I am having problem when running the Monte Carlo script. The script > seems to fail after only a few simulations but it does not give me any > error message, it just says 'killed'. I am running it on 126 > participants (2 groups of 63) and I have tried it on a number of > different measures (sulc, area etc.). I thought it may be an space > issue but I cleared all other files but that did not seem to make any > difference. > > This is what is printed out on the terminal: > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdirRh_JacobianW_15
> --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite > > cmdline mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh--fsgd
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgddods
> --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > --surf fsaverage rh --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label--C
>/projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat
> --C >/projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat
> > > > WARNING: unrecognized mri_glmfit cmd option dods > > > SURFACE: fsaverage rh > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign > neg --overwrite > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ > > Thu Apr 24 18:58:31 IST 2014 > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > fitzgeje > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > DoPoll = 0 > > DoPBSubmit = 0 > > DoBackground = 0 > > DiagCluster = 0 > > gd2mtx = dods > > fwhm = 21.770250 > > nSimPerJob = 10000 > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> --C >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > --fsgd Rh_JacobianW_15/y.fsgd dods --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > --surf fsaverage rh white > > INFO: ignoring tag Creator > > INFO: ignoring tag SUBJECTS_DIR > > INFO: ignoring tag SynthSeed > > reading group avg surface area 822 cm^2 from file > > Reading in average area >/projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
> > reading group avg surface area 822 cm^2 from file > > Reading in average area >/projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
> > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 groupASD > > 2 groupCTRL > > INFO: gd2mtx_method is dods > > Reading source surface > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65020.765625 > > AvgVtxArea 0.396850 > > AvgVtxDist 0.717994 > > StdVtxDist 0.193566 > > INFO: fwhm2niters: NOT fixing group surface area > > Surface smoothing by fwhm=21.770250, niters=441.000000 > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > cmdline mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> --C >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > --fsgd Rh_JacobianW_15/y.fsgd dods --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > --surf fsaverage rh white > > sysname Linux > > hostname lonsdale01.cluster > > machine x86_64 > > user fitzgeje > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > fwhm 21.770250 > > niters 441.000000 > > OneSampleGroupMean 0 > > y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > logyflag 0 > > usedti 0 > > FSGD Rh_JacobianW_15/y.fsgd > > labelmask > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > mask Rh_JacobianW_15/mask.mgh > > maskinv 0 > > glmdir (null) > > IllCondOK 0 > > DoFFx 0 > > Loading y from > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > INFO: gd2mtx_method is dods > > Matrix condition is 1 > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > Found 149926 points in label. > > Found 149926 voxels in mask > > search space = 75188.6 > > DOF = 124 > > thresh = 1.3, threshadj = 0.99897 > > > > Starting simulation sim over 10000 trials > > Smoothing done, nsteps = 441, tsec = 69.733 > > Smoothing done, nsteps = 441, tsec = 69.799 > > Smoothing done, nsteps = 441, tsec = 69.754 > > Smoothing done, nsteps = 441, tsec = 69.749 > > Smoothing done, nsteps = 441, tsec = 69.743 > > Smoothing done, nsteps = 441, tsec = 69.749 > > Smoothing done, nsteps = 441, tsec = 69.737 > > Smoothing done, nsteps = 441, tsec = 69.738 > > Smoothing done, nsteps = 441, tsec = 69.734 > > Smoothing done, nsteps = 441, tsec = 69.806 > > Smoothing done, nsteps = 441, tsec = 70.012 > > Smoothing done, nsteps = 441, tsec = 70.139 > > > Killed > > > Any suggestions that may help? > > Kind regards, > > Jackie > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Jacqueline Fitzgerald PhD Candidate Department of Psychiatry / Trinity Institute of Neuroscience Room 3.36b Lloyd Building Trinity College Dublin Dublin 2
Tel: (01) 896 4102
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what version are you using? There is also help when you run mri_glmfit-sim --help
On 04/29/2014 08:10 AM, Jacqueline Elaine Fitzgerald wrote:
Hi Doug,
I had not realised that was possible, thanks for that. Will save alot of time! I am getting an error that the --cache flag is not recognised. This is the command I am running;
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15 --cache 2.3 neg --cwp 0.05 ERROR: Flag --cache unrecognized.
Is there an additional directory or step I need to do?
Thanks again for your help,
Best,
Jackie
On 28 April 2014 18:11, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, I mean using the --cache option which will use precomputed tables rather than generating new ones On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote: > Hi Doug, > > Thank you for your reply. By precomputed do you mean the FDR in the > GUI? Apologies I'm still new to the program! > > I am planning on running an ROI analysis so will need to run it for > that anyway (I think?) > > Best, > > Jackie > > > On 24 April 2014 21:47, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > First of all, do you really need to run the simulation? If you are > just > doing a whole hemisphere analysis on fsaverage, then you can use the > precomputed option. > > doug > > On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > > Hi, > > > > I am having problem when running the Monte Carlo script. The script > > seems to fail after only a few simulations but it does not give > me any > > error message, it just says 'killed'. I am running it on 126 > > participants (2 groups of 63) and I have tried it on a number of > > different measures (sulc, area etc.). I thought it may be an space > > issue but I cleared all other files but that did not seem to > make any > > difference. > > > > This is what is printed out on the terminal: > > > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 > > --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite > > > > cmdline mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods > > --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > > --surf fsaverage rh --label > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat > > --C > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat > > > > > > > > WARNING: unrecognized mri_glmfit cmd option dods > > > > > > SURFACE: fsaverage rh > > > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > > > --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative > --sim-sign > > neg --overwrite > > > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ > > > > Thu Apr 24 18:58:31 IST 2014 > > > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed > Oct 16 > > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > fitzgeje > > > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > > > DoPoll = 0 > > > > DoPBSubmit = 0 > > > > DoBackground = 0 > > > > DiagCluster = 0 > > > > gd2mtx = dods > > > > fwhm = 21.770250 > > > > nSimPerJob = 10000 > > > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > > > mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > > --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm > 21.770250 > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > --surf fsaverage rh white > > > > INFO: ignoring tag Creator > > > > INFO: ignoring tag SUBJECTS_DIR > > > > INFO: ignoring tag SynthSeed > > > > reading group avg surface area 822 cm^2 from file > > > > Reading in average area > > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > > > reading group avg surface area 822 cm^2 from file > > > > Reading in average area > > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > > > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > > > INFO: demeaning continous variables > > > > Continuous Variable Means (all subjects) > > > > Class Means of each Continuous Variable > > > > 1 groupASD > > > > 2 groupCTRL > > > > INFO: gd2mtx_method is dods > > > > Reading source surface > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > > > Number of vertices 163842 > > > > Number of faces 327680 > > > > Total area 65020.765625 > > > > AvgVtxArea 0.396850 > > > > AvgVtxDist 0.717994 > > > > StdVtxDist 0.193566 > > > > INFO: fwhm2niters: NOT fixing group surface area > > > > Surface smoothing by fwhm=21.770250, niters=441.000000 > > > > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > > > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > > > cmdline mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > > --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm > 21.770250 > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > --surf fsaverage rh white > > > > sysname Linux > > > > hostname lonsdale01.cluster > > > > machine x86_64 > > > > user fitzgeje > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing 1 > > > > fwhm 21.770250 > > > > niters 441.000000 > > > > OneSampleGroupMean 0 > > > > y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > > > logyflag 0 > > > > usedti 0 > > > > FSGD Rh_JacobianW_15/y.fsgd > > > > labelmask > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > mask Rh_JacobianW_15/mask.mgh > > > > maskinv 0 > > > > glmdir (null) > > > > IllCondOK 0 > > > > DoFFx 0 > > > > Loading y from > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Matrix condition is 1 > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > Found 149926 points in label. > > > > Found 149926 voxels in mask > > > > search space = 75188.6 > > > > DOF = 124 > > > > thresh = 1.3, threshadj = 0.99897 > > > > > > > > Starting simulation sim over 10000 trials > > > > Smoothing done, nsteps = 441, tsec = 69.733 > > > > Smoothing done, nsteps = 441, tsec = 69.799 > > > > Smoothing done, nsteps = 441, tsec = 69.754 > > > > Smoothing done, nsteps = 441, tsec = 69.749 > > > > Smoothing done, nsteps = 441, tsec = 69.743 > > > > Smoothing done, nsteps = 441, tsec = 69.749 > > > > Smoothing done, nsteps = 441, tsec = 69.737 > > > > Smoothing done, nsteps = 441, tsec = 69.738 > > > > Smoothing done, nsteps = 441, tsec = 69.734 > > > > Smoothing done, nsteps = 441, tsec = 69.806 > > > > Smoothing done, nsteps = 441, tsec = 70.012 > > > > Smoothing done, nsteps = 441, tsec = 70.139 > > > > > > Killed > > > > > > Any suggestions that may help? > > > > Kind regards, > > > > Jackie > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > > -- > Jacqueline Fitzgerald > PhD Candidate > Department of Psychiatry / Trinity Institute of Neuroscience > Room 3.36b Lloyd Building > Trinity College Dublin > Dublin 2 > > Tel: (01) 896 4102 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Jacqueline Fitzgerald PhD Candidate Department of Psychiatry / Trinity Institute of Neuroscience Room 3.36b Lloyd Building Trinity College Dublin Dublin 2
Tel: (01) 896 4102
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm using version 4.5.0. The --cache does not come up when I type the command mri_glmfit-sim --help?
Best,
Jackie
On 29 April 2014 16:58, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
what version are you using? There is also help when you run mri_glmfit-sim --help
On 04/29/2014 08:10 AM, Jacqueline Elaine Fitzgerald wrote:
Hi Doug,
I had not realised that was possible, thanks for that. Will save alot of time! I am getting an error that the --cache flag is not recognised. This is the command I am running;
[fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15 --cache 2.3 neg --cwp 0.05 ERROR: Flag --cache unrecognized.
Is there an additional directory or step I need to do?
Thanks again for your help,
Best,
Jackie
On 28 April 2014 18:11, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, I mean using the --cache option which will use precomputed tables rather than generating new ones On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote: > Hi Doug, > > Thank you for your reply. By precomputed do you mean the FDR in the > GUI? Apologies I'm still new to the program! > > I am planning on running an ROI analysis so will need to run it for > that anyway (I think?) > > Best, > > Jackie > > > On 24 April 2014 21:47, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > First of all, do you really need to run the simulation? If you are > just > doing a whole hemisphere analysis on fsaverage, then you can use the > precomputed option. > > doug > > On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > > Hi, > > > > I am having problem when running the Monte Carlo script. The script > > seems to fail after only a few simulations but it does not give > me any > > error message, it just says 'killed'. I am running it on 126 > > participants (2 groups of 63) and I have tried it on a number of > > different measures (sulc, area etc.). I thought it may be an space > > issue but I cleared all other files but that did not seem to > make any > > difference. > > > > This is what is printed out on the terminal: > > > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 > > --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite > > > > cmdline mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgddods
> > --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > > --surf fsaverage rh --label > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label--C
> > >/projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat
> > --C > > >/projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat
> > > > > > > > WARNING: unrecognized mri_glmfit cmd option dods > > > > > > SURFACE: fsaverage rh > > > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > > > --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative > --sim-sign > > neg --overwrite > > > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp$
> > > > Thu Apr 24 18:58:31 IST 2014 > > > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMPWed
> Oct 16 > > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > fitzgeje > > > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > > > DoPoll = 0 > > > > DoPBSubmit = 0 > > > > DoBackground = 0 > > > > DiagCluster = 0 > > > > gd2mtx = dods > > > > fwhm = 21.770250 > > > > nSimPerJob = 10000 > > > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > > > mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> > --C > > >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm > 21.770250 > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > --surf fsaverage rh white > > > > INFO: ignoring tag Creator > > > > INFO: ignoring tag SUBJECTS_DIR > > > > INFO: ignoring tag SynthSeed > > > > reading group avg surface area 822 cm^2 from file > > > > Reading in average area > > >/projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
> > > > reading group avg surface area 822 cm^2 from file > > > > Reading in average area > > >/projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
> > > > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > > > INFO: demeaning continous variables > > > > Continuous Variable Means (all subjects) > > > > Class Means of each Continuous Variable > > > > 1 groupASD > > > > 2 groupCTRL > > > > INFO: gd2mtx_method is dods > > > > Reading source surface > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > > > Number of vertices 163842 > > > > Number of faces 327680 > > > > Total area 65020.765625 > > > > AvgVtxArea 0.396850 > > > > AvgVtxDist 0.717994 > > > > StdVtxDist 0.193566 > > > > INFO: fwhm2niters: NOT fixing group surface area > > > > Surface smoothing by fwhm=21.770250, niters=441.000000 > > > > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp$
> > > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > > > cmdline mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> > --C > > >Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm > 21.770250 > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > --surf fsaverage rh white > > > > sysname Linux > > > > hostname lonsdale01.cluster > > > > machine x86_64 > > > > user fitzgeje > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing 1 > > > > fwhm 21.770250 > > > > niters 441.000000 > > > > OneSampleGroupMean 0 > > > > y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > > > logyflag 0 > > > > usedti 0 > > > > FSGD Rh_JacobianW_15/y.fsgd > > > > labelmask > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > mask Rh_JacobianW_15/mask.mgh > > > > maskinv 0 > > > > glmdir (null) > > > > IllCondOK 0 > > > > DoFFx 0 > > > > Loading y from > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Matrix condition is 1 > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > Found 149926 points in label. > > > > Found 149926 voxels in mask > > > > search space = 75188.6 > > > > DOF = 124 > > > > thresh = 1.3, threshadj = 0.99897 > > > > > > > > Starting simulation sim over 10000 trials > > > > Smoothing done, nsteps = 441, tsec = 69.733 > > > > Smoothing done, nsteps = 441, tsec = 69.799 > > > > Smoothing done, nsteps = 441, tsec = 69.754 > > > > Smoothing done, nsteps = 441, tsec = 69.749 > > > > Smoothing done, nsteps = 441, tsec = 69.743 > > > > Smoothing done, nsteps = 441, tsec = 69.749 > > > > Smoothing done, nsteps = 441, tsec = 69.737 > > > > Smoothing done, nsteps = 441, tsec = 69.738 > > > > Smoothing done, nsteps = 441, tsec = 69.734 > > > > Smoothing done, nsteps = 441, tsec = 69.806 > > > > Smoothing done, nsteps = 441, tsec = 70.012 > > > > Smoothing done, nsteps = 441, tsec = 70.139 > > > > > > Killed > > > > > > Any suggestions that may help? > > > > Kind regards, > > > > Jackie > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > > -- > Jacqueline Fitzgerald > PhD Candidate > Department of Psychiatry / Trinity Institute of Neuroscience > Room 3.36b Lloyd Building > Trinity College Dublin > Dublin 2 > > Tel: (01) 896 4102 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Jacqueline Fitzgerald PhD Candidate Department of Psychiatry / Trinity Institute of Neuroscience Room 3.36b Lloyd Building Trinity College Dublin Dublin 2
Tel: (01) 896 4102
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Upgrade! You can run the glm analysis in a new version and keep the old version for your individual analysis doug
On 04/29/2014 01:06 PM, Jacqueline Elaine Fitzgerald wrote:
I'm using version 4.5.0. The --cache does not come up when I type the command mri_glmfit-sim --help?
Best,
Jackie
On 29 April 2014 16:58, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what version are you using? There is also help when you run mri_glmfit-sim --help On 04/29/2014 08:10 AM, Jacqueline Elaine Fitzgerald wrote: > Hi Doug, > > I had not realised that was possible, thanks for that. Will save alot > of time! I am getting an error that the --cache flag is not > recognised. This is the command I am running; > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15 > --cache 2.3 neg --cwp 0.05 > ERROR: Flag --cache unrecognized. > > Is there an additional directory or step I need to do? > > Thanks again for your help, > > Best, > > Jackie > > > > > On 28 April 2014 18:11, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > No, I mean using the --cache option which will use precomputed tables > rather than generating new ones > > On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote: > > Hi Doug, > > > > Thank you for your reply. By precomputed do you mean the FDR in the > > GUI? Apologies I'm still new to the program! > > > > I am planning on running an ROI analysis so will need to run it for > > that anyway (I think?) > > > > Best, > > > > Jackie > > > > > > On 24 April 2014 21:47, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > First of all, do you really need to run the simulation? If > you are > > just > > doing a whole hemisphere analysis on fsaverage, then you can > use the > > precomputed option. > > > > doug > > > > On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > > > Hi, > > > > > > I am having problem when running the Monte Carlo script. > The script > > > seems to fail after only a few simulations but it does not > give > > me any > > > error message, it just says 'killed'. I am running it on 126 > > > participants (2 groups of 63) and I have tried it on a > number of > > > different measures (sulc, area etc.). I thought it may be > an space > > > issue but I cleared all other files but that did not seem to > > make any > > > difference. > > > > > > This is what is printed out on the terminal: > > > > > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir > Rh_JacobianW_15 > > > --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite > > > > > > cmdline mri_glmfit --y > > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd > > > > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods > > > --glmdir > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > > > --surf fsaverage rh --label > > > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C > > > > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat > > > --C > > > > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat > > > > > > > > > > > > WARNING: unrecognized mri_glmfit cmd option dods > > > > > > > > > SURFACE: fsaverage rh > > > > > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > > > > > --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative > > --sim-sign > > > neg --overwrite > > > > > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ > > > > > > Thu Apr 24 18:58:31 IST 2014 > > > > > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed > > Oct 16 > > > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > fitzgeje > > > > > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > > > > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > > > > > DoPoll = 0 > > > > > > DoPBSubmit = 0 > > > > > > DoBackground = 0 > > > > > > DiagCluster = 0 > > > > > > gd2mtx = dods > > > > > > fwhm = 21.770250 > > > > > > nSimPerJob = 10000 > > > > > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > > > > > mri_glmfit --y > > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > > > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > > > --C > > > > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm > > 21.770250 > > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > --surf fsaverage rh white > > > > > > INFO: ignoring tag Creator > > > > > > INFO: ignoring tag SUBJECTS_DIR > > > > > > INFO: ignoring tag SynthSeed > > > > > > reading group avg surface area 822 cm^2 from file > > > > > > Reading in average area > > > > > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > > > > > reading group avg surface area 822 cm^2 from file > > > > > > Reading in average area > > > > > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > > > > > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > > > > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > > > > > INFO: demeaning continous variables > > > > > > Continuous Variable Means (all subjects) > > > > > > Class Means of each Continuous Variable > > > > > > 1 groupASD > > > > > > 2 groupCTRL > > > > > > INFO: gd2mtx_method is dods > > > > > > Reading source surface > > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > > > > > Number of vertices 163842 > > > > > > Number of faces 327680 > > > > > > Total area 65020.765625 > > > > > > AvgVtxArea 0.396850 > > > > > > AvgVtxDist 0.717994 > > > > > > StdVtxDist 0.193566 > > > > > > INFO: fwhm2niters: NOT fixing group surface area > > > > > > Surface smoothing by fwhm=21.770250, niters=441.000000 > > > > > > > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > > > > > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > > > > > cmdline mri_glmfit --y > > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > > > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > > > --C > > > > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3 > > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm > > 21.770250 > > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > --surf fsaverage rh white > > > > > > sysname Linux > > > > > > hostname lonsdale01.cluster > > > > > > machine x86_64 > > > > > > user fitzgeje > > > > > > FixVertexAreaFlag = 1 > > > > > > UseMaskWithSmoothing 1 > > > > > > fwhm 21.770250 > > > > > > niters 441.000000 > > > > > > OneSampleGroupMean 0 > > > > > > y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > > > > > logyflag 0 > > > > > > usedti 0 > > > > > > FSGD Rh_JacobianW_15/y.fsgd > > > > > > labelmask > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > > > mask Rh_JacobianW_15/mask.mgh > > > > > > maskinv 0 > > > > > > glmdir (null) > > > > > > IllCondOK 0 > > > > > > DoFFx 0 > > > > > > Loading y from > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > > > > > INFO: gd2mtx_method is dods > > > > > > Matrix condition is 1 > > > > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > > > > > Found 149926 points in label. > > > > > > Found 149926 voxels in mask > > > > > > search space = 75188.6 > > > > > > DOF = 124 > > > > > > thresh = 1.3, threshadj = 0.99897 > > > > > > > > > > > > Starting simulation sim over 10000 trials > > > > > > Smoothing done, nsteps = 441, tsec = 69.733 > > > > > > Smoothing done, nsteps = 441, tsec = 69.799 > > > > > > Smoothing done, nsteps = 441, tsec = 69.754 > > > > > > Smoothing done, nsteps = 441, tsec = 69.749 > > > > > > Smoothing done, nsteps = 441, tsec = 69.743 > > > > > > Smoothing done, nsteps = 441, tsec = 69.749 > > > > > > Smoothing done, nsteps = 441, tsec = 69.737 > > > > > > Smoothing done, nsteps = 441, tsec = 69.738 > > > > > > Smoothing done, nsteps = 441, tsec = 69.734 > > > > > > Smoothing done, nsteps = 441, tsec = 69.806 > > > > > > Smoothing done, nsteps = 441, tsec = 70.012 > > > > > > Smoothing done, nsteps = 441, tsec = 70.139 > > > > > > > > > Killed > > > > > > > > > Any suggestions that may help? > > > > > > Kind regards, > > > > > > Jackie > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > > > -- > > Jacqueline Fitzgerald > > PhD Candidate > > Department of Psychiatry / Trinity Institute of Neuroscience > > Room 3.36b Lloyd Building > > Trinity College Dublin > > Dublin 2 > > > > Tel: (01) 896 4102 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Jacqueline Fitzgerald > PhD Candidate > Department of Psychiatry / Trinity Institute of Neuroscience > Room 3.36b Lloyd Building > Trinity College Dublin > Dublin 2 > > Tel: (01) 896 4102 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Jacqueline Fitzgerald PhD Candidate Department of Psychiatry / Trinity Institute of Neuroscience Room 3.36b Lloyd Building Trinity College Dublin Dublin 2
Tel: (01) 896 4102
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Douglas N Greve -
Jacqueline Elaine Fitzgerald