Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

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 <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>
<mailto:greve@nmr.mgh.harvard.edu
<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 <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>>>
>     >
>     >
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>     >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
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>
> --
> *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>>
>
>
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--
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>
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-- *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

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