Hello
I typed in the command for multiple comparison: $ mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos
It starts to process, but there is an error (see below). How do I fix this? Thanks, Jenny
mdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir SURFACE: average rh log file is rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir/cache.mri_glmfit-sim.log
cd /study4/NCCAM/Data/MRI/processed/structural/freesurfer /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos
$Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Thu Jul 12 15:24:55 CDT 2012 Linux balsa.keck.waisman.wisc.edu 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 09:58:09 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux jliu setenv SUBJECTS_DIR /study/NCCAM/Data/MRI/processed/structural/freesurfer FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest
Original mri_glmfit command line: cmdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.724818 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd
Also, in addition to the mri_glmfit-sim command,
I have already run the mris_preproc, mri_surf2surf, and mri_glmfit before typing mri_glmfit-sim. Did I miss a step? Do I need to update an app?
Thanks, Jenny
On Thu, Jul 12, 2012 at 3:28 PM, Jenny Liu liujenny23@gmail.com wrote:
Hello
I typed in the command for multiple comparison: $ mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos
It starts to process, but there is an error (see below). How do I fix this? Thanks, Jenny
mdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir SURFACE: average rh log file is rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir/cache.mri_glmfit-sim.log
cd /study4/NCCAM/Data/MRI/processed/structural/freesurfer /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos
$Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Thu Jul 12 15:24:55 CDT 2012 Linux balsa.keck.waisman.wisc.edu 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 09:58:09 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux jliu setenv SUBJECTS_DIR /study/NCCAM/Data/MRI/processed/structural/freesurfer FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest
Original mri_glmfit command line: cmdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.724818 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd
Hmmm, that is strange. It's the same error as my previous email. Can you verify that the file below exists and that you can read it? /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd
On 07/12/2012 04:28 PM, Jenny Liu wrote:
Hello
I typed in the command for multiple comparison: $ mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos
It starts to process, but there is an error (see below). How do I fix this? Thanks, Jenny
mdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir SURFACE: average rh log file is rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir/cache.mri_glmfit-sim.log
cd /study4/NCCAM/Data/MRI/processed/structural/freesurfer /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos
$Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Thu Jul 12 15:24:55 CDT 2012 Linux balsa.keck.waisman.wisc.edu http://balsa.keck.waisman.wisc.edu 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 09:58:09 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux jliu setenv SUBJECTS_DIR /study/NCCAM/Data/MRI/processed/structural/freesurfer FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest
Original mri_glmfit command line: cmdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.724818 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Jenny Liu