Hello:
Freesurfers, follow the tutorial '
* FsTutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial * GroupAnalysishttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?action=fullsearch&context=180&value=linkto%3A%22FsTutorial/GroupAnalysis%22', my task is to find the thickness differences between groups(Controls(30) & AD(30)), and it works well for the first part which is to fit the linear model and get the uncorrected P_values, and I got the expected P-value map, but when I followed the clusterwise correction for multiple comparision, with this command below:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces
I got two questions: 1) with the flag --2spaces, i got the error that this command not found; 2) also, with or without the --2spaces, after the freeview open, i got another error, which said did not find any volume geometry information in the surface, I googled, and I know Doug has answered in this post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, but I think my freesurfer is the newest version:freesurfer-5.3.0-15052013-x86_64-centos!
As below, these are my command and the output:
§§Command: export SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE mri_glmfit-sim \ --glmdir lh.AD_CN_NO_COVARIATE.glmdir \ --cache 1.3 neg \ --cwp 0.05\ --2spaces
# load the cluster annotation in freeview freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot -viewport 3d
§§Output:
cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir SURFACE: fsaverage lh log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log
cd /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim --glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 26 16:20:39 CEST 2016 Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux wen setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ FREESURFER_HOME /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos
Original mri_glmfit command line: cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 22.776285 CSD /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh --csd /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd --mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --vwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.voxel.mgh --sum lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary --ocn lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --oannot lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot --annot aparc --csdpdf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.pdf.dat --cwpvalthresh 0.05 --o lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh --no-fixmni --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 1.3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh MGH ocnid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh MGH sumfile = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary subjectsdir = /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/surf/lh.white Done reading source surface Reading annotation /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149955 Done loading source values (nvtxs = 163842) overall max = 8.58718 at vertex 22205 overall min = -1.57802 at vertex 24019 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 0/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 2 clusters Max cluster size 132.153870 Pruning by CW P-Value 0.05 Saving thresholded output to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh Saving cluster numbers to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh Saving cluster pval lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2688
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2688 sysname Linux hostname HP1973 machine x86_64 user wen UseRobust 0 Loading lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh Loading /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation
Reporting on 0 segmentations Computing spatial average of each frame
Writing to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat mri_segstats done mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --frame 0 mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 0 writing to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh... Thu May 26 16:20:39 CEST 2016 Thu May 26 16:20:45 CEST 2016 mri_glmfit-sim done ./cluster_wise_correction_for_multiple_comparisons.sh: line 23: --2spaces: command not found Did not find any volume geometry information in the surface p-Breading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none)
Can you give me some answer? Thank you very much!