On 02/11/2016 11:19 AM, Jennifer Legault wrote: > Thank you for your response. Do I need to run the glm_fit-sim command > to make the csd file? I feel this would be inappropriate for my data > since I already ran the LME model. No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will need the FWHM though > > Second, is there an argument to make an output file that can be > visualized via freeview? In other words, how can I view my cluster > thresholded data? You can use freeview, something like freeview -f lh.inflated:overlay=sig.mgh There are other options for loading annotations and curvature. See the freeview help > > Your help is greatly appreciated, > > Jen > > > > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve > <[email protected] <mailto:[email protected]>> wrote: > > There is a (very long) command line on that page. Mainly you need > a csd file. To get that you need the FWHM of your analysis, the > voxel-wise threshold, and the sign of the contrast (or abs). Then > the relevant output will be the --sum. You can run it with --help > to get more info. > > > On 2/10/16 5:11 PM, Jennifer Legault wrote: >> Thank you very much for your help! I still received a "cannot >> read file type" error when I only added the path to the output >> --o part, however when I also added the path to the input file, >> it worked! >> >> I do have one more question: Which argument can I add so that in >> my output file I see the clusterwise P value, like it is shown >> here >> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary>? >> >> Best, >> >> Jen >> >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve >> <[email protected] <mailto:[email protected]>> wrote: >> >> I meant for the output files, so the --o in particular >> >> On 02/10/2016 01:47 PM, Jennifer Legault wrote: >> > Douglas, >> > >> > Thank you for your quick response. When I add --sd >> [path_location], I >> > get the following error: >> > Loading source values >> > mri_read(): couldn't determine type of file >> [path_location]/rh_time_spval >> > ERROR: could not read rh_time_spval as type >> > >> > Should I use another argument? >> > >> > Best, >> > >> > Jen >> > >> > >> > >> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve >> > <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> wrote: >> > >> > Try specifying the full path to the output >> > >> > On 02/10/2016 12:59 PM, Jennifer Legault wrote: >> > > Dear experts, >> > > >> > > I am trying to use the cluster thresholding command >> for my >> > freesurfer >> > > LME outputs as referred to here >> > > >> > >> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>. >> > > Any feedback or comments would be greatly appreciated. >> > > >> > > I am aware that there have been permission denied >> errors when using >> > > mri_surfcluster and that applying this patch >> > > >> > >> >> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg> >> > > should solve the problem (which I tried), however I >> am still either >> > > receiving errors stating the permission is denied. >> > > >> > > This is the command I am trying to run: >> > > >> > > mri_surfcluster --subject fsaverage --hemi rh --in >> > rh_time_spval.mgh >> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o >> rh_time_cluster --sum >> > > rh_time_cluster_sum >> > > >> > > >> > > Here is the error log: >> > > >> > > mri_surfcluster --subject fsaverage --hemi rh --in >> rh_time_spval.mgh >> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o >> rh_time_cluster --sum >> > > rh_time_cluster_sum thsign = pos, id = 1 >> > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 >> 22:10:05 >> > greve Exp $ >> > > hemi = rh >> > > srcid = rh_time_spval.mgh >> > > srcsubjid = fsaverage >> > > srcsurf = white >> > > srcframe = 0 >> > > thsign = pos >> > > thmin = -1 >> > > thmax = -1 >> > > fdr = 0.05 >> > > minarea = 0 >> > > xfmfile = talairach.xfm >> > > nth = -1 >> > > outid = rh_time_cluster paint >> > > sumfile = rh_time_cluster_sum >> > > subjectsdir = /gpfs/home/jtl190/work/structurals >> > > FixMNI = 1 >> > > ------------- XFM matrix (RAS2RAS) --------------- >> > > >> > >> >> /gpfs/home/jtl190/work/structurals/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 >> > > >> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white >> > > Done reading source surface >> > > Computing metric properties >> > > Loading source values >> > > number of voxels in search space = 163842 >> > > Done loading source values (nvtxs = 163842) >> > > overall max = 1 at vertex 27 >> > > overall min = 1.52021e-05 at vertex 125620 >> > > surface nvertices 163842 >> > > surface area 65020.929688 >> > > surface area 65020.765625 >> > > Setting voxel-wise threshold with FDR = 0.050000 >> > > Assuming input map is -log10(p) >> > > MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, >> vwth=1.04576 >> > > FDR Voxel-wise threshold is 1.04576 >> > > Adjusting threshold for 1-tailed test. >> > > If the input is not a -log10(p) volume, re-run with >> --no-adjust. >> > > Searching for Clusters ... >> > > thmin=1.045757 (0.744727), thmax=-1.000000 (-1), >> thsignid=1, >> > > minarea=0.000000 >> > > Found 9803 clusters >> > > Max cluster size 5993.586426 >> > > INFO: fixing MNI talairach coordinates >> > > Saving thresholded output to rh_time_cluster >> > > Can't create file >> > > >> > >> >> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w >> > > >> > > Permission denied >> > > >> > > >> > > >> > > >> > > Thank you for taking the time to read this email. >> > > >> > > Sincerely, >> > > >> > > Jennifer Legault >> > > >> > > -- >> > > Jennifer Legault >> > > Ph.D candidate, Neuroscience >> > > Brain, Language, and Computation Lab >> > > The Pennsylvania State University >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > [email protected] >> <mailto:[email protected]> >> > <mailto:[email protected] >> <mailto:[email protected]>> >> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> <tel:617-726-7422>> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> > 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. >> > >> > >> > >> > >> > -- >> > Jennifer Legault >> > Ph.D candidate, Neuroscience >> > Brain, Language, and Computation Lab >> > The Pennsylvania State University >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > [email protected] >> <mailto:[email protected]> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] <mailto:[email protected]> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> -- >> Jennifer Legault >> Ph.D candidate, Neuroscience >> Brain, Language, and Computation Lab >> The Pennsylvania State University >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > 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. > > > > > -- > Jennifer Legault > Ph.D candidate, Neuroscience > Brain, Language, and Computation Lab > The Pennsylvania State University > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
