External Email - Use Caution I'm using version 6.0.0.
2020년 8월 20일 (목) 오전 12:08, Douglas N. Greve <dgr...@mgh.harvard.edu>님이 작성: > what version of fs are you using? > > On 8/19/2020 9:03 AM, 정현우 wrote: > > 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 > > > _______________________________________________ > 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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