Hi: Because I make the group analysis with SurfStat, and I get the cluster after the clusterwise correction, so I think in Freesurfer, we should have the similiar result:)
________________________________________ 发件人: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> 代表 Douglas N Greve <gr...@nmr.mgh.harvard.edu> 发送时间: 2016年5月26日 18:22:58 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim why do you think there shold be a cluster? On 05/26/2016 12:21 PM, Hao wen wrote: > Hi, > I tried every value for the --cache and --cwp, as what i understood, the > --cache is the threshold for the vertex-wise correction and the --cwp is the > clusterwise correction, and i even tried the 0.99 with the --cwp, which > should give me all my cluster, but still, I got nothing, I checked the > 'mri_glmfit-sim', and it seems not so clear for me, do you there where is the > problem? > > Merci > Hao > ________________________________________ > 发件人: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> 代表 Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > 发送时间: 2016年5月26日 17:54:58 > 收件人: freesurfer@nmr.mgh.harvard.edu > 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim > > It looks like it worked. there is not an error there. It did not find > any voxels above your chosen level of signficance, but that is not an > error per se > > On 05/26/2016 11:19 AM, Hao wen wrote: >> Doug: >> >> Thank you for your reply, it does not work, also, I think the problem >> is that for me after the clusterwise correction, I got no corrected >> cluster, I am not sure if it the problem that I set the --cache value >> and the --cwp value, but I changed the value, it always return me nothing! >> >> This is the msg, it said that found 0 value : >> >> >> 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 0.001 >> 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 >> >> >> Do you have any idea? >> >> Best >> >> Hao >> >> ------------------------------------------------------------------------ >> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> 代表 Douglas Greve >> <gr...@nmr.mgh.harvard.edu> >> *发送时间:* 2016年5月26日 17:06:48 >> *收件人:* freesurfer@nmr.mgh.harvard.edu >> *主题:* Re: [Freesurfer] Cluster-wise correction error with >> mri_glmfit-sim >> Instead of --2spaces, use --bonferroni 2 >> >> On 5/26/16 10:30 AM, Hao wen wrote: >>> Hello: >>> >>> Freesurfers, follow the tutorial ' >>> >>> # FsTutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial> >>> # GroupAnalysis >>> <https://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�CBreading 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! >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://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 > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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