you need to add --cache threshold sign (and don't use --sim-sign or --sim)
On 10/20/2014 05:42 PM, Thomas DeRamus wrote:
> It does not I'm afraid. The error I get says the following:
>
> mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
> --sim-sign abs --2spaces
> ERROR: must spec --sim
>
> Does the same if I remove the --sim-sign abs as well.
>
> On Mon, Oct 20, 2014 at 3:15 PM, Douglas N Greve
> <mailto:greve@nmr.mgh.harvard.edu> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
> You should not spec --sim. If you do not, does it work?
> doug
>
> On 10/20/2014 04:10 PM, Thomas DeRamus wrote:
> > I guess the better term would be to say that I'm not sure if the
> > cluster correction is using the monte-carlo I made from the
> label file
> > correctly.
> >
> > I see on the wiki and in the mailing list you can use a different
> > directory and then spec that folder using mri_glmfit-sim with the
> > --cache-dir flag. When I run it like that, I get this output
> > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
> > --cwp 0.05 --2spaces --sim
> > ERROR: flag --sim requires four arguments
> >
> > When I specify the sim (which I'm not sure I need since I ran the
> > simulation already) and sim-sign abs, and run either of the
> following,
> > I get these as outputs:
> >
> > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z
> > 10000 2
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
> > --sim-sign abs --2spacescmdline mri_glmfit --y
> > rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd
> > SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C
> > agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C
> > ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label
> > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> > --glmdir rh.ALESocial__agevolume.glmdir
> > SURFACE: fsaverage rh
> > log file is
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > cd /media/rkbatch/gyrification
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > /usr/local/freesurfer/bin/mri_glmfit-sim
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 10000 2
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
> > --sim-sign abs --2spaces
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > Mon Oct 20 15:06:19 CDT 2014
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC
> > 2012 x86_64 x86_64 x86_64 GNU/Linux
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > tderamus
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > setenv SUBJECTS_DIR /media/rkbatch/gyrification
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > FREESURFER_HOME /usr/local/freesurfer
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > Original mri_glmfit command line:
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh
> > --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx
> > --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C
> > ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label
> > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> > --glmdir rh.ALESocial__agevolume.glmdir
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > DoSim = 1
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > UseCache = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > DoPoll = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > DoPBSubmit = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > DoBackground = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > DiagCluster = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > gd2mtx = dods
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > fwhm = 14.594354
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > nSimPerJob = 10000
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > 1/1 Mon Oct 20 15:06:19 CDT 2014
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > mri_glmfit --y
> >
> /media/rkbatch/gyrification/rh.diagnosisxageICVslopetest.volume.10.mgh
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/agesxdiagnosisnonlGI.mtx
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/diagnosisnonlGIICmeas.mtx
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/diagnosisnonxagexICmeas.mtx
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/ICmeasurexdiagnosisnonlGI.mtx
> > --mask rh.ALESocial__agevolume.glmdir/mask.mgh --sim mc-z 10000 2
> >
> rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.j001
> > --sim-sign abs --fwhm 14.594354 --fsgd
> > rh.ALESocial__agevolume.glmdir/y.fsgd dods --label
> > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> --surf
> > fsaverage rh white
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log:
> > No such file or directory
> > INFO: ignoring tag Creator
> > INFO: ignoring tag SUBJECTS_DIR
> > INFO: ignoring tag SynthSeed
> > MatrixMultiply: m1 is null!
> >
> > No such file or directory
> > simbase
> >
> rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.j001
> > FWHM = 14.594354
> > gdfReadHeader: reading rh.ALESocial__agevolume.glmdir/y.fsgd
> > INFO: NOT demeaning continuous variables
> > Continuous Variable Means (all subjects)
> > 0 Age 18.4329 6.76585
> > 1 tICV 1.67822e+06 146117
> > Class Means of each Continuous Variable
> > 1 CTRL 18.2315 1690205.3333
> > 2 ASD 18.6525 1665138.7273
> >
> > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z
> > 10000 2
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd
> > --sim-sign abs --2spaces
> > cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh
> > --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx
> > --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C
> > ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label
> > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> > --glmdir rh.ALESocial__agevolume.glmdir
> > SURFACE: fsaverage rh
> > log file is
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > cd /media/rkbatch/gyrification
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > /usr/local/freesurfer/bin/mri_glmfit-sim
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 10000 2
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd
> > --sim-sign abs --2spaces
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > Mon Oct 20 15:04:37 CDT 2014
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC
> > 2012 x86_64 x86_64 x86_64 GNU/Linux
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > tderamus
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > setenv SUBJECTS_DIR /media/rkbatch/gyrification
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > FREESURFER_HOME /usr/local/freesurfer
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > Original mri_glmfit command line:
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh
> > --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx
> > --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C
> > ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label
> > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> > --glmdir rh.ALESocial__agevolume.glmdir
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> >
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > DoSim = 1
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > UseCache = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > DoPoll = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > DoPBSubmit = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > DoBackground = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > DiagCluster = 0
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > gd2mtx = dods
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > fwhm = 14.594354
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > nSimPerJob = 10000
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > 1/1 Mon Oct 20 15:04:37 CDT 2014
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > mri_glmfit --y
> >
> /media/rkbatch/gyrification/rh.diagnosisxageICVslopetest.volume.10.mgh
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/agesxdiagnosisnonlGI.mtx
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/diagnosisnonlGIICmeas.mtx
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/diagnosisnonxagexICmeas.mtx
> > --C
> >
> rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/ICmeasurexdiagnosisnonlGI.mtx
> > --mask rh.ALESocial__agevolume.glmdir/mask.mgh --sim mc-z 10000 2
> >
> rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.j001
> > --sim-sign abs --fwhm 14.594354 --fsgd
> > rh.ALESocial__agevolume.glmdir/y.fsgd dods --label
> > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> --surf
> > fsaverage rh white
> > tee:
> >
> rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log:
> > No such file or directory
> > INFO: ignoring tag Creator
> > INFO: ignoring tag SUBJECTS_DIR
> > INFO: ignoring tag SynthSeed
> > MatrixMultiply: m1 is null!
> >
> > No such file or directory
> > simbase
> >
> rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.j001
> > FWHM = 14.594354
> > gdfReadHeader: reading rh.ALESocial__agevolume.glmdir/y.fsgd
> > INFO: NOT demeaning continuous variables
> > Continuous Variable Means (all subjects)
> > 0 Age 18.4329 6.76585
> > 1 tICV 1.67822e+06 146117
> > Class Means of each Continuous Variable
> > 1 CTRL 18.2315 1690205.3333
> > 2 ASD 18.6525 1665138.7273
> >
> > Since the directory and flags are returning errors, I'm assuming I'm
> > just inputing everything incorrectly or its a path issue. Does
> that help?
> >
> > On Mon, Oct 20, 2014 at 2:53 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <tel:205-934-0971>> <tel:205-934-0971 <tel:205-934-0971>> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> >
> > what do you mean it has trouble understanding? What is your
> > command line
> > and terminal output. Also, are you following these instructions?
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
> >
> >
> > On 10/20/2014 03:50 PM, Thomas DeRamus wrote:
> > > Dear Freesurfer Experts,
> > >
> > > I have a label file of a number of ROI's I've made based
> on a mask.
> > > I'm trying to get an idea of what cluster are significant
> within a
> > > focused region of the label file.
> > >
> > > To make the correction a little less sever, I pre-computed
> some
> > > monte-carlo values using mri_mcsim
> > >
> > > mri_mcsim --o
> > >
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain
> > > --base mc-z --surface fsaverage rh --nreps 10000 --label
> > > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> > >
> > > mri_mcsim --o
> > > $SUBJECTS_DIR/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain
> > --base
> > > mc-z --surface fsaverage lh --nreps 10000 --label
> > > $SUBJECTS_DIR/fsaverage/label/lh.SocialBrainMask
> > >
> > > Respectively for each surface (the labels are different on
> each
> > > hemisphere).
> > >
> > > I've run mri_glmfit and have the uncorrected outputs and
> results
> > > (there are actually 6 of these, one for volume, thickness, and
> > surface
> > > area for each hemi):
> > >
> > > mri_glmfit --y
> rh.diagnosisxagexrightThickslopetest.thickness.10.mgh
> > > --fsgd SBM_glmRightthickNOGENDER.fsgd dods --C
> > > diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C
> > > diagnosisnonxagexICmeas.mtx --C
> ICmeasurexdiagnosisnonlGI.mtx --surf
> > > fsaverage rh --label
> > > /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> > > --glmdir rh.ALESocial__agethickness.glmdir
> > >
> > > But when I try to do the mri_glmfit-sim, I am having
> trouble getting
> > > it to read in the corrected csd file.
> > >
> > > I'm wanting to run it at cwp of 0.05 at a threshold of 2
> (0.01),
> > with
> > > a correction for two hemispheres. However, when I try to
> run it with
> > > --cache-dir
> > >
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain
> > > , it has trouble understanding the --cwp .05, --2spaces
> and 2 abs
> > > (after cache dir) flags. Additionally, it wants a --sim and
> > --sim-sign
> > > value like it wants to compute a monte-carlo from scratch.
> > >
> > > Could I get an example on how best to direct it to the
> > simulation I've
> > > run on it?
> > >
> > > Thanks much.
> > > -Thomas
> > >
> > >
> > > --
> > > *Thomas DeRamus*
> > > UAB Department of Psychology, Behavioral Neuroscience
> > > Graduate Research Trainee
> > > Civitan International Research Center
> > > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
> > > _Phone_: 205-934-0971 <tel:205-934-0971> <tel:205-934-0971
> > <tel:205-934-0971 <tel:205-934-0971>>> _Email:_ tpderamus@gmail.com
> <mailto:tpderamus@gmail.com>
> > <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>>
> > > <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>
> <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>>>,
> > faustus@uab.edu <mailto:faustus@uab.edu> <mailto:faustus@uab.edu
> <mailto:faustus@uab.edu>> <mailto:faustus@uab.edu
> <mailto:faustus@uab.edu>
> > <mailto:faustus@uab.edu <mailto:faustus@uab.edu>>>
> > >
> > >
> > > _______________________________________________
> > > 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.
> >
> >
> >
> >
> > --
> > *Thomas DeRamus*
> > UAB Department of Psychology, Behavioral Neuroscience
> > Graduate Research Trainee
> > Civitan International Research Center
> > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
> > _Phone_: 205-934-0971 <tel:205-934-0971> _Email:_
> tpderamus@gmail.com <mailto:tpderamus@gmail.com>
> > <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>>,
> faustus@uab.edu <mailto:faustus@uab.edu> <mailto:faustus@uab.edu
> <mailto:faustus@uab.edu>>
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
> --
> *Thomas DeRamus*
> UAB Department of Psychology, Behavioral Neuroscience
> Graduate Research Trainee
> Civitan International Research Center
> 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
> _Phone_: 205-934-0971 _Email:_ tpderamus@gmail.com
> <mailto:tpderamus@gmail.com>, faustus@uab.edu <mailto:faustus@uab.edu>
>
>
> _______________________________________________
> 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/
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