1 Sep
2020
1 Sep
'20
3:02 p.m.
You do not need to re-run recon-all. You can use v6 recon-all output with v7 mris_preproc, mri_glmfit, mri_glmfit-sim, and fspalm
On 9/1/2020 11:56 AM, 정현우 wrote:
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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 <dgreve@mgh.harvard.edu mailto:dgreve@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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-forceWhat 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/MultipleComparisonsV6.0PermSo 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 pathfspalm --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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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