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.
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? Your help is greatly appreciated, Jen On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> 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 < > gr...@nmr.mgh.harvard.edu> 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 >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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 >> > > Freesurfer@nmr.mgh.harvard.edu >> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> > 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 >> > Freesurfer@nmr.mgh.harvard.edu <mailto: >> 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. >> > >> > >> > >> > >> > -- >> > Jennifer Legault >> > Ph.D candidate, Neuroscience >> > Brain, Language, and Computation Lab >> > The Pennsylvania State University >> > >> > >> > _______________________________________________ >> > 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 >> > > > > -- > Jennifer Legault > Ph.D candidate, Neuroscience > Brain, Language, and Computation Lab > The Pennsylvania State University > > > _______________________________________________ > 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 > > > 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 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.
