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
