Thanks! I'll try that. Mihaela On Fri, May 29, 2015 at 12:20 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote:
> The clusterwise p-value (--cwp) will correspond to a certain cluster > size, so you can play with that to get clusters of a certain size. In the > vbm example you give below, each of those clusters will have a p-value, > they just choose not to report them. > doug > > > On 5/29/15 11:50 AM, Mihaela Stefan wrote: > > Hi Doug, > > The simulation went smoothly, however, as I suspected, no clusters were > detected. I wonder if you have any thoughts about my question in the > previous email, regarding the uncorrected p values. > > Thanks! > Mihaela > > On Thu, May 28, 2015 at 11:09 AM, Mihaela Stefan <mikaelastep...@gmail.com > > wrote: > >> Thanks, Doug, the command seems to work. I guess it will take a while to >> finish running. >> >> On a different note, I have a large data set that doesn't seem to >> generate corrected results. What's interesting is that the uncorrected >> results are consistent with our previous findings and those from the >> related literature, using smaller samples (but the technique used was VBM >> not surface analysis). >> >> In FreeSurfer, I used FDR and Monte Carlo so far with different p >> values for cluster forming threshold and clusterwise p-value. Nothing >> survived the correction. Now I am trying the permutation but I'm not too >> optimistic. So I was wondering if there's a way to report uncorrected >> p-values with a surface analysis in FreeSurfer. I know that's possible for >> VBM, where some people used uncorrected p<0.001 with a cluster size of 30 >> voxels or p<0.005 with a cluster size of 60 voxels. Is there an equivalent >> of this in FreeSurfer? >> >> Thanks! >> Mihaela >> >> On Wed, May 27, 2015 at 5:33 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> Right, strictly speaking, permutationis for orthogonal design matrices >>> only, which is not the case when you have a covariate. There was a >>> recent paper by Anderson Winkler "Permutation Inference for the General >>> Linear Model" in NI in which he goes over various permutation methods >>> for non-orthogonal designs, one of which is to pretend that it is >>> orthogonal (--perm-force). I don't know whether it is appropriate for >>> your design or not. >>> doug >>> >>> >>> On 05/27/2015 04:37 PM, Mihaela Stefan wrote: >>> > Thanks! It seems that there was a white space. I ran the permutation >>> > command but now I got another error: >>> > >>> > ERROR: design matrix is not orthogonal, cannot be used with >>> permutation. >>> > If this something you really want to do, run with --perm-force >>> > Wed May 27 16:27:50 EDT 2015 >>> > ERROR: cannot find any csd files >>> > >>> > I did a group difference like here (first contrast): >>> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V >>> > >>> > Best, >>> > Mihaela >>> > >>> > >>> > On Wed, May 27, 2015 at 4:18 PM, Douglas N Greve >>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> > >>> > Are you sure there is not any white space after the backslash (\)? >>> > If so, Can you run it with --debug as the first option? >>> > >>> > On 05/27/2015 03:39 PM, Mihaela Stefan wrote: >>> > > Hello FreeSurfers, >>> > > >>> > > I am trying to run a clusterwise correction following this link: >>> > > >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >>> > > >>> > > I would like to use the permutation simulation instead of Z Monte >>> > > Carlo. I ran mri_glmfit-sim --help to get more information. >>> > > >>> > > Following an example, I ran this command: mri_glmfit-sim \ >>> > > --glmdir lh.g2v1.glmdir \ >>> > > --sim perm 5000 1.3 perm.neg.13 --sim-sign neg >>> > > Then I got an error which says: --sim: Command not found. >>> > > >>> > > I tried again using the exact example in the help info: >>> > mri_glmfit-sim >>> > > --glmdir lh.g2v1.glmdir \ >>> > > --sim mc-z 10000 3 mc-z.neg.3 --sim-sign neg >>> > > However, I get the same error: --sim: Command not found. >>> > > >>> > > Does anyone know why I get this error? >>> > > >>> > > Thanks! >>> > > Mihaela >>> > > >>> > > >>> > > _______________________________________________ >>> > > 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. >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > 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 >>> >> >> > > > _______________________________________________ > 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. > >
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