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 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 _Email:_ tpderamus@gmail.com mailto:tpderamus@gmail.com, faustus@uab.edu mailto:faustus@uab.edu
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