External Email - Use Caution
Dear Douglas,
I was wondering if you might be able to take another look at my request
below. Unfortunately, I still haven't been able to resolve the issue
when I try to run mri_glmfit-sim. The error seems to be with
mri_surfcluster.bin. I was wondering if you might have any advice.
Please see the error message below.
Thank you again,
Colleen
Starting simulation sim over 1000 trials
mri_glmfit simulation done 63.5672
Thu Jan 31 10:34:16 GMT 2019
mri_surfcluster --in lh.lgi_300119.glmdir/NH-H/sig.mgh --mask
lh.lgi_300119.glmdir/mask.mgh --cwsig
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.cluster.mgh --sum
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.cluster.summary --ocn
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.ocn.mgh --annot aparc
--cwpvalthresh 0.05 --o
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.masked.mgh --no-fixmni --csd
lh.lgi_300119.glmdir/csd/perm.th20.abs.j001-NH-H.csd --csdpdf
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.pdf.dat --vwsig
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.voxel.mgh --vwsigmax
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.voxel.max.dat --oannot
lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.ocn.annot --bonferroni 2
--surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi = lh
srcid = lh.lgi_300119.glmdir/NH-H/sig.mgh
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = abs
thmin = 2
thmax = -1
fdr = -1
minarea = 0
Bonferroni = 2
xfmfile = talairach.xfm
nth = -1
outid = lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.masked.mgh MGH
ocnid = lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.ocn.mgh MGH
sumfile = lh.lgi_300119.glmdir/NH-H/perm.th20.abs.sig.cluster.summary
subjectsdir = /home/cper2/scratch/Freesurfer/Beijing
FixMNI = 0
Found 148421 vertices in mask
Found 148421 vertices in mask
Found 148421 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/home/cper2/scratch/Freesurfer/Beijing/fsaverage/mri/transforms/talairach.xfm
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
MRISread(\ufffd\ufffd\ufffd): could not open file
No such file or directory
----------------------------------------------------
Reading source surface
/home/cper2/scratch/Freesurfer/Beijing/fsaverage/surf/lh.white
mri_surfcluster.bin: could not read surface
/home/cper2/scratch/Freesurfer/Beijing/fsaverage/surf/lh.white
No such file or directory
-------- Original Message --------
Subject: Re: mri_glmfit-sim error correcting for MC for LGI analysis
Date: 2018-11-27 11:46
From: "C.P.E. Rollins" <cp...@cam.ac.uk>
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Hi Douglas,
Thanks a lot for your answers.
1) For the permutations, would you recommend using this for controlling
for MC in cortical thickness analyses too? Why is it recommended to use
permutation simulation as opposed to Z Monte Carlo simulation for an LGI
analysis?
2) I've attached here the output from ls -Rl
$FREESURFER_HOME/subjects/fsaverage.
Thanks again,
Colleen
On 2018-11-23 16:26, C.P.E. Rollins wrote:
Dear Freesurfer Developers,
I have a 2-part question:
1) I was advised to use permutation to control for multiple
comparisons in an LGI analysis, would you mind elaborating how to do
this in command line (in terms of command and parameters)?
2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
(attached). I was wondering if you might have any advice? The file
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
view it in freeview.
Many thanks,
Colleen
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage:
total 169
drwxrwsr-x 2 pfb29 sysadmin 125 Dec 21 2015 label
drwxrwsr-x 4 pfb29 sysadmin 21 Nov 27 2012 mri
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drwxrwsr-x 2 pfb29 sysadmin 18 Nov 13 2015 scripts
drwxrwsr-x 2 pfb29 sysadmin 68 Nov 13 2015 surf
drwxrwsr-x 12 pfb29 sysadmin 16 Nov 13 2015 xhemi
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lh.Yeo2011_7NetworksConfidence_N1000.mgz
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lh.Yeo2011_7Networks_N1000.annot
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lh.Yeo_Brainmap_10to14Comp_Flexibility.mgz
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lh.Yeo_Brainmap_10to14Comp_SpecializationROI.mgz
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lh.Yeo_Brainmap_10to14Comp_TopSpecializationComp.csv
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lh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz
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lh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz
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rh.Yeo2011_7NetworksConfidence_N1000.mgz
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rh.Yeo2011_7Networks_N1000.annot
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rh.Yeo_Brainmap_10Comp_PrActGivenComp.mgz
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rh.Yeo_Brainmap_10to14Comp_Specialization.mgz
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rh.Yeo_Brainmap_10to14Comp_SpecializationROI.mgz
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rh.Yeo_Brainmap_10to14Comp_TopSpecializationComp.csv
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rh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz
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rh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz
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rh.Yeo_Brainmap_13Comp_PrActGivenComp.mgz
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rh.Yeo_Brainmap_14Comp_PrActGivenComp.mgz
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/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/mri:
total 21628
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/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/mri/transforms:
total 38
drwxrwsr-x 2 pfb29 sysadmin 2 Dec 30 2010 bak
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/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/scripts:
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/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/surf:
total 175741
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-rwxrwxr-x 1 pfb29 sysadmin 655672 Aug 14 2007 lh.orig.avg.area.mgh
-rwxrwxr-x 1 pfb29 sysadmin 5898808 Apr 11 2013 lh.pial
-rwxrwxr-x 1 pfb29 sysadmin 5898567 Aug 14 2007 lh.pial_avg
-rwxrwxr-x 1 pfb29 sysadmin 655672 Aug 14 2007 lh.pial.avg.area.mgh
-rwxrwxr-x 1 pfb29 sysadmin 5898794 Jan 9 2014 lh.pial_semi_inflated
-rwxrwxr-x 1 pfb29 sysadmin 5899169 Apr 11 2013 lh.smoothwm
-rwxrwxr-x 1 pfb29 sysadmin 5898546 Aug 14 2007 lh.sphere
-rwxrwxr-x 1 pfb29 sysadmin 5898771 Nov 13 2015 lh.sphere.left_right
-rwxrwxr-x 1 pfb29 sysadmin 5898546 Aug 14 2007 lh.sphere.reg
-rwxrwxr-x 1 pfb29 sysadmin 5898551 Aug 14 2007 lh.sphere.reg.avg
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 16 2007 lh.sulc
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 lh.thickness
-rwxrwxr-x 1 pfb29 sysadmin 5898808 Apr 11 2013 lh.white
-rwxrwxr-x 1 pfb29 sysadmin 5898567 Aug 14 2007 lh.white_avg
-rwxrwxr-x 1 pfb29 sysadmin 655672 Aug 14 2007 lh.white.avg.area.mgh
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 lh.white_avg.H
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 lh.white_avg.K
-rwxrwxr-x 1 pfb29 sysadmin 58940 Aug 14 2007 mris_preproc.surface.lh.log
-rwxrwxr-x 1 pfb29 sysadmin 58945 Aug 14 2007 mris_preproc.surface.rh.log
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.area
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.avg_curv
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 16 2007 rh.avg_sulc
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.avg_thickness
-rwxrwxr-x 1 pfb29 sysadmin 2396248 Jun 19 2008 rh.cortex.patch.3d
-rwxrwxr-x 1 pfb29 sysadmin 2396248 Jun 19 2008 rh.cortex.patch.flat
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.curv
-rwxrwxr-x 1 pfb29 sysadmin 5899402 Nov 13 2015 rh.fsaverage_sym.sphere.reg
-rwxrwxr-x 1 pfb29 sysadmin 5899528 Apr 11 2013 rh.inflated
-rwxrwxr-x 1 pfb29 sysadmin 5898567 Aug 14 2007 rh.inflated_avg
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.inflated.H
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.inflated.K
-rwxrwxr-x 1 pfb29 sysadmin 5899285 Aug 14 2007 rh.inflated_pre
-rwxrwxr-x 1 pfb29 sysadmin 5898808 Apr 11 2013 rh.orig
-rwxrwxr-x 1 pfb29 sysadmin 5898567 Aug 14 2007 rh.orig_avg
-rwxrwxr-x 1 pfb29 sysadmin 655672 Aug 14 2007 rh.orig.avg.area.mgh
-rwxrwxr-x 1 pfb29 sysadmin 5898808 Apr 11 2013 rh.pial
-rwxrwxr-x 1 pfb29 sysadmin 5898567 Aug 14 2007 rh.pial_avg
-rwxrwxr-x 1 pfb29 sysadmin 655672 Aug 14 2007 rh.pial.avg.area.mgh
-rwxrwxr-x 1 pfb29 sysadmin 5898794 Jan 9 2014 rh.pial_semi_inflated
-rwxrwxr-x 1 pfb29 sysadmin 5899169 Apr 11 2013 rh.smoothwm
-rwxrwxr-x 1 pfb29 sysadmin 5898546 Aug 14 2007 rh.sphere
-rwxrwxr-x 1 pfb29 sysadmin 5898771 Nov 13 2015 rh.sphere.left_right
-rwxrwxr-x 1 pfb29 sysadmin 5898546 Aug 14 2007 rh.sphere.reg
-rwxrwxr-x 1 pfb29 sysadmin 5898551 Aug 14 2007 rh.sphere.reg.avg
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 16 2007 rh.sulc
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.thickness
-rwxrwxr-x 1 pfb29 sysadmin 5898808 Apr 11 2013 rh.white
-rwxrwxr-x 1 pfb29 sysadmin 5898567 Aug 14 2007 rh.white_avg
-rwxrwxr-x 1 pfb29 sysadmin 655672 Aug 14 2007 rh.white.avg.area.mgh
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.white_avg.H
-rwxrwxr-x 1 pfb29 sysadmin 655383 Aug 14 2007 rh.white_avg.K
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi:
total 247
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 bem
drwxrwsr-x 2 pfb29 sysadmin 8 Nov 13 2015 label
-rwxrwxr-x 1 pfb29 sysadmin 64 Nov 13 2015 lrrev.pure.register.dat
-rwxrwxr-x 1 pfb29 sysadmin 64 Nov 13 2015 lrrev.register.dat
drwxrwsr-x 4 pfb29 sysadmin 12 Nov 13 2015 mri
drwxrwsr-x 2 pfb29 sysadmin 13 Nov 13 2015 scripts
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 src
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 stats
drwxrwsr-x 2 pfb29 sysadmin 28 Nov 13 2015 surf
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 tmp
drwxrwsr-x 2 pfb29 sysadmin 3 Nov 13 2015 touch
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 trash
-rwxrwxr-x 1 pfb29 sysadmin 45999 Nov 13 2015 xhemireg.lh.log
-rwxrwxr-x 1 pfb29 sysadmin 13219 Nov 13 2015 xhemireg.rh.log
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/bem:
total 0
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/label:
total 9226
-rwxrwxr-x 1 pfb29 sysadmin 1314060 Nov 13 2015 lh.aparc.a2009s.annot
-rwxrwxr-x 1 pfb29 sysadmin 1312250 Nov 13 2015 lh.aparc.annot
-rwxrwxr-x 1 pfb29 sysadmin 5964904 Nov 13 2015 lh.cortex.label
-rwxrwxr-x 1 pfb29 sysadmin 1314060 Nov 13 2015 rh.aparc.a2009s.annot
-rwxrwxr-x 1 pfb29 sysadmin 1312250 Nov 13 2015 rh.aparc.annot
-rwxrwxr-x 1 pfb29 sysadmin 6117569 Nov 13 2015 rh.cortex.label
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/mri:
total 20142
-rwxrwxr-x 1 pfb29 sysadmin 341423 Nov 13 2015 aparc+aseg.mgz
-rwxrwxr-x 1 pfb29 sysadmin 365159 Nov 13 2015 aseg.mgz
-rwxrwxr-x 1 pfb29 sysadmin 1862531 Nov 13 2015 brainmask.mgz
-rwxrwxr-x 1 pfb29 sysadmin 1862531 Nov 13 2015 brain.mgz
-rwxrwxr-x 1 pfb29 sysadmin 21734 Nov 13 2015 mri_nu_correct.mni.log
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 orig
-rwxrwxr-x 1 pfb29 sysadmin 5247514 Nov 13 2015 orig.mgz
-rwxrwxr-x 1 pfb29 sysadmin 5769705 Nov 13 2015 orig_nu.mgz
-rwxrwxr-x 1 pfb29 sysadmin 4926479 Nov 13 2015 T1.mgz
drwxrwsr-x 3 pfb29 sysadmin 7 Nov 13 2015 transforms
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/mri/orig:
total 0
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/mri/transforms:
total 85
drwxrwsr-x 2 pfb29 sysadmin 2 Nov 13 2015 bak
-rwxrwxr-x 1 pfb29 sysadmin 191 Nov 13 2015 talairach.auto.xfm
-rwxrwxr-x 1 pfb29 sysadmin 83122 Nov 13 2015 talairach_avi.log
-rwxrwxr-x 1 pfb29 sysadmin 191 Nov 13 2015 talairach.xfm
-rwxrwxr-x 1 pfb29 sysadmin 385 Nov 13 2015
talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/mri/transforms/bak:
total 0
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/scripts:
total 307
-rwxrwxr-x 1 pfb29 sysadmin 50 Nov 13 2015 build-stamp.txt
-rwxrwxr-x 1 pfb29 sysadmin 50 Nov 13 2015 lastcall.build-stamp.txt
-rwxrwxr-x 1 pfb29 sysadmin 0 Nov 13 2015 patchdir.txt
-rwxrwxr-x 1 pfb29 sysadmin 504 Nov 13 2015 recon-all.cmd
-rwxrwxr-x 1 pfb29 sysadmin 501 Nov 13 2015 recon-all.done
-rwxrwxr-x 1 pfb29 sysadmin 6688 Nov 13 2015 recon-all.env
-rwxrwxr-x 1 pfb29 sysadmin 317862 Nov 13 2015 recon-all.local-copy
-rwxrwxr-x 1 pfb29 sysadmin 38945 Nov 13 2015 recon-all.log
-rwxrwxr-x 1 pfb29 sysadmin 182 Nov 13 2015 recon-all-status.log
-rwxrwxr-x 1 pfb29 sysadmin 62678 Nov 13 2015 surfreg.fsaverage_sym.lh.log
-rwxrwxr-x 1 pfb29 sysadmin 4389 Nov 13 2015 surfreg.fsaverage_sym.rh.log
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/src:
total 0
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/stats:
total 0
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/surf:
total 73319
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 lh.area
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 lh.curv
-rwxrwxr-x 1 pfb29 sysadmin 5899506 Nov 13 2015 lh.fsaverage_sym.sphere.reg
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 lh.inflated
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 lh.inflated.H
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 lh.inflated.K
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 lh.orig
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 lh.pial
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 lh.smoothwm
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 lh.sphere
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 lh.sulc
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 lh.thickness
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 lh.white
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.area
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.curv
-rwxrwxr-x 1 pfb29 sysadmin 5899506 Nov 13 2015 rh.fsaverage_sym.sphere.reg
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 rh.inflated
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.inflated.H
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.inflated.K
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 rh.orig
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 rh.pial
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 rh.smoothwm
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 rh.sphere
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.sulc
-rwxrwxr-x 1 pfb29 sysadmin 655383 Nov 13 2015 rh.thickness
-rwxrwxr-x 1 pfb29 sysadmin 5898862 Nov 13 2015 rh.white
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/tmp:
total 0
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/touch:
total 10
-rwxrwxr-x 1 pfb29 sysadmin 58 Nov 13 2015 talairach.touch
/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/xhemi/trash:
total 0
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