Hi Douglas, Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD file and I selected the fwhm01 csd file.
I then ran the mri_surfcluster command, however, I got the following error: ERROR: you have specified srcsubjid=fsaverage on cmdline, but CSD file was created with fsaverage Any suggestions you have would be appreciated. Best, Jen On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 > -- 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.
