Those seem to be giving the "must specify sim" error as well I'm afraid.
mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-label /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ ERROR: must spec --sim
/media/rkbatch/gyrification $ mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/ --cache-label rh.Socialbrain ERROR: must spec --sim
/media/rkbatch/gyrification $ mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-label rh.Socialbrain ERROR: must spec --sim
Also is cache-label its own flag or does it need to include the cache-dir or something else?
On Tue, Oct 21, 2014 at 11:45 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
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>>> 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 <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 --glmdirrh.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>>>> 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 NGreve
> > > <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 > > > > --glmdirrh.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:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>
> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%3E
> > > 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 <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, AL35233
> > > _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>>> > > > <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>> > > 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 > > <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