by "volume" do you mean a VBM-type analysis or do you mean the volume that comes out of FS (thickness*area)? If you are going to use a clusterwise correction, then you have to have a FWHM measurement. You can try analyzing it in mri_glmfit with --osgm just to get the FWHM out of it.
You should be able to output a .mgh file instead of a .w file On 02/11/2016 01:07 PM, Jennifer Legault wrote: > That's very useful, thank you. In terms of FWHM, I am examining gray > matter volume, not cortical thickness, and was previously instructed > by Martin Reuter not to smooth these data. Do you think it would make > sense then to just use the fwhm01? And in terms of the voxel-wise > threshold, is there a commonly used value for GM volume data? I am > still new to freesurfer and I appreciate any feedback. > > For visualization, after I run the mri_surfcluster the only outputs > are a summary file and a .w file, and freeview doesn't accept this > format. Is it possible to have a cluster-wise corrected map (a > sig.cluster.mgh file) as they do for the Clusterwise Correction for > Multiple Comparisons tutorial here > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>? > > > Best, > > Jen > > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto: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> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto: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> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > >> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > >> <tel: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>> <tel: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> > >> > > <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> > >> > > >> > <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> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > >> 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 > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 list > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > <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 > Fax: 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 > > > > > -- > 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
