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 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> 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> 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>>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>>> 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-z10000 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-z10000 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>>>> 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 amhaving
> 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>>>> _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>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > -- > > *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>>>, > faustus@uab.edu <mailto:faustus@uab.edu> <mailto:faustus@uab.edu <mailto:faustus@uab.edu>> <mailto:faustus@uab.edu <mailto:faustus@uab.edu> > <mailto:faustus@uab.edu <mailto:faustus@uab.edu>>> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > *Thomas DeRamus* > UAB Department of Psychology, Behavioral Neuroscience > Graduate Research Trainee > Civitan International Research Center > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 > _Phone_: 205-934-0971 <tel:205-934-0971> _Email:_ tpderamus@gmail.com <mailto:tpderamus@gmail.com> > <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>>, faustus@uab.edu <mailto:faustus@uab.edu> <mailto:faustus@uab.edu <mailto:faustus@uab.edu>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 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
-- *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, faustus@uab.edu