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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" cper2@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