sorry it is --cache-label
On 10/21/2014 12:40 PM, Thomas DeRamus wrote:
> And if you remove it it just goes back to the "must specify sim" error.
>
> On Tue, Oct 21, 2014 at 11:39 AM, Thomas DeRamus <tpderamus@gmail.com
> <mailto:tpderamus@gmail.com>> wrote:
>
> It says the label flag is unrecognized.
>
> mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/ --label
> rh.Socialbrain
> ERROR: Flag --label unrecognized.
> --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/ --label
> rh.Socialbrain
>
>
> On Tue, Oct 21, 2014 at 11:30 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> I think you need to pass it
> --cache-dir
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor --label
> rh.SocialBrainMask
>
> doug
>
> On 10/21/2014 10:31 AM, Thomas DeRamus wrote:
> > How do I change the path so that it's reading from the label
> I made
> > (Socialbrain) in lieu of the cortex?
> >
> > On Mon, Oct 20, 2014 at 5:42 PM, Thomas DeRamus
> <tpderamus@gmail.com <mailto:tpderamus@gmail.com>
> > <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>>>
> <mailto:greve@nmr.mgh.harvard.edu> wrote:
> >
> > That one gives the following error:
> >
> > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir
> --cache-dir
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
> > --cache 2 abs
> > 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/cache.mri_glmfit-sim.log
> >
> > cd /media/rkbatch/gyrification
> > /usr/local/freesurfer/bin/mri_glmfit-sim
> > --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
> > --cache 2 abs
> >
> > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve
> Exp $
> > Mon Oct 20 17:39:34 CDT 2014
> > 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
> > tderamus
> > setenv SUBJECTS_DIR /media/rkbatch/gyrification
> > FREESURFER_HOME /usr/local/freesurfer
> >
> > Original mri_glmfit command line:
> > 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
> >
> > DoSim = 0
> > UseCache = 1
> > DoPoll = 0
> > DoPBSubmit = 0
> > DoBackground = 0
> > DiagCluster = 0
> > gd2mtx = dods
> > fwhm = 14.594354
> > ERROR: cannot find
> >
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain//fsaverage/rh/cortex/fwhm15/abs/th20/mc-z.csd
> >
> >
> > It looks like its still trying to use the cached
> monte-carlo from
> > the fsaverage rather than the one for the label. Am I using
> > --cache-dir correctly?
> >
> > On Mon, Oct 20, 2014 at 5:34 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > 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>
> > <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
> <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>>
> > <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
> <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:
> > > >
> > > >
> > > > 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>>> <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 <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> <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>>>
> > > > <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
> <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>
> > <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
> <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>>>
> > <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
> <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> <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 <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>>
> > > <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
> <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>>>
> > > <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:Freesurfer@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>
> > > >
> > <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>
> > > >
> >
> <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>>>
> <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.
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > *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>> _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>>>
> > > Fax: 617-726-7422 <tel:617-726-7422>> > > > <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
> <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>>>
> > <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
> <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>>
> > > <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:617-726-7422
> > <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
> > >
> > >
> > >
> > >
> > > --
> > > *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>>
> > > <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>
> > Fax: 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
> >
> >
> >
> >
> > --
> > *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>
> > <mailto:tpderamus@gmail.com
> <mailto:tpderamus@gmail.com>>, faustus@uab.edu
> <mailto:faustus@uab.edu> <mailto:faustus@uab.edu
> <mailto:faustus@uab.edu>>
> >
> >
> >
> >
> > --
> > *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>
> > <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
> 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
>
>
>
>
> --
> *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>
>
>
>
>
> --
> *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/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer