External Email - Use Caution Hi Douglas,
Thank you for your advice. I just wanted to make sure what I should expect before installing v7.1.1 - will v7.1.1 allow me to run commands for analyses (e.g. mri_glmfit, mri_glmfit-sim, fspalm) with the recon-all outputs from v6.0.0? Or will I have to run recon-all for all study subjects again with the new version? Thanks, Hyunwoo 2020년 8월 20일 (목) 오후 10:42, Douglas N. Greve <dgr...@mgh.harvard.edu>님이 작성: > I think we made some changes in v7.1.1 that might fix the error. Can you > try that? I suspect the underlying problem is that there are not any > clusters that are surviving > > On 8/19/2020 11:11 AM, 정현우 wrote: > > 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 > > > _______________________________________________ > 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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