External Email - Use Caution Hi Douglas,
Thank you for your response. I followed your suggestions and additionally tried using Matlab instead of Octave for FsPalm analysis, but I still failed to get the results. Adding $FREESURFER_HOME/fsfast/toolbox to my matlab path removed the first error output <error: 'fast_p2z' undefined near line 1 column 11>, but I still get the other error output <error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz" - check for run_palm.m failures'>. Do you have any suggestions for this problem? Thanks, Hyunwoo 2020년 8월 13일 (목) 오후 10:37, Douglas N. Greve <dgr...@mgh.harvard.edu>님이 작성: > > > On 8/12/2020 2:44 AM, 정현우 wrote: > > External Email - Use Caution > Hello Freesurfer Developers, > > I'm trying to do permutation simulation on 50 subjects to find brain > region clusters of which cortical thicknesses have significant association > with clinical parameters while controlling for age and sex. I tried this > via 'mri_glmfit-sim' but it seems that permutation analysis could not be > done with non-orthogonal variables in Freesurfer. I copied the command I > used and the error output below. > > mri_glmfit-sim --glmdir NK_IES_avoidance_correlation.rh.glmdir --perm 1000 > 1.3 abs --cwp 0.05 --2spaces > > ERROR: design matrix is not orthogonal, cannot be used with permutation. > If this something you really want to do, run with --perm-force > > What version of FS are you using? If Version 6, then make sure you > download the patch. See "If You're Not in an organized course" from > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm > > > So I tried using PALM, which allows permutation analysis with > non-orthogonal variables according to a post in the Freesurfer Archive. I > installed PALM, FsPalm and Octave on my computer and ran the command below, > but I ran into another error output (copied below) that I do not quite > understand. > > You need to add $FREESURFER_HOME/fsfast/toolbox to your matlab path > > > fspalm --glmdir NK_IES_avoidance_correlation.rh.glmdir --cft 1.3 --twotail > --name perm.NK_IES_avoidance_correlation.rh --iters 1000 --2spaces --cwp > .05 --octave > > preparing a palm subdirectory in > /media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.glmdir/perm.NK_IES_avoidance_correlation.rh > found NK_IES_avoidance_correlation.rh.glmdir/surface file - this is a > surface-based analysis > using the glmfit input file > /media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.10.mgh > using area file > /media/sjkim/hd2/subject_data/fsaverage/surf/rh.white.avg.area.mgh > palm prep complete - running the generated matlab script... > error: 'fast_p2z' undefined near line 1 column 11 > error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz" - > check for run_palm.m failures > > I copied the matlab script 'run_palm.m' below. > > hemi = 'rh'; > input = > '/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.10.mgh'; > maskfile = > '/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.glmdir/mask.mgh'; > surffile = '/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white'; > areafile = > '/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white.avg.area.mgh'; > > %% Changing threshold for two-tailed test > cft = 1.3 + 0.301; > pthresh = 10^-cft; > zthresh = fast_p2z(pthresh); > iters = 1000; > > zthreshstr = sprintf('%f',zthresh); > itersstr = sprintf('%d',iters); > > > palm('-i',input,'-m',maskfile,'-d','design.mat','-t','design.con','-logp',... > '-n',itersstr,'-C',zthreshstr,'-o','fsp','-twotail','-s',surffile, > areafile); > return; > > Do you have any suggestions on how I could figure out this problem? Of > note, I am using Freesurfer v6.0 and Ubuntu 18.04.4 LTS platform. > > Thanks in advance, > Hyunwoo Jeong > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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