Sorry, the summary file is not what you want. Can you send a list of the files in the folder? doug
On 02/24/2014 11:26 AM, Douglas N Greve wrote: > > what version of FS are you using? there should be a file with > "summary" in the name. Also, try looking at the help with > mri_glmfit-sim --help > doug > > > On 02/21/2014 11:39 PM, charujing123 wrote: >> Hi doug, >> I tried to generate the mean thickness of the cluster in uncorrected >> p value<0.005 for each subject by this command "mri_glmfit-sim >> --glmdir lh.score.dir --cwp 1 --cache 2.3 neg". It generates some >> files named with suffix >> ".pdf.dat,cluster.mgh,cluster.summary,masked.mgh,ocn.annot,ocn.mgh,voxel.mgh". >> >> I cannot find a file that can tell me the mean thickness for each >> subject. Did I miss something? >> Thanks. >> All the best. >> Rujing Zha >> 2014-02-22 >> ------------------------------------------------------------------------ >> charujing123 >> ------------------------------------------------------------------------ >> *发件人：*"charujing123"<charujing...@163.com> >> *发送时间：*2014-02-22 10:08 >> *主题：*Re: [Freesurfer] extracting mean thickness from specific cluster >> *收件 人：*"freesurfer@nmr.mgh.harvard.edu" >> <freesurfer@nmr.mgh.harvard.edu> >> *抄送：* >> Hi doug and others, >> Thanks doug. >> For 1st question:I find that file. However not all has that file.May >> I generate it manually? >> Thanks doug. >> All the best. >> Rujing Zha >> 2014-02-22 >> ------------------------------------------------------------------------ >> charujing123 >> ------------------------------------------------------------------------ >> *发件人：*Douglas Greve <gr...@nmr.mgh.harvard.edu> >> *发送时间：*2014-02-21 23:46 >> *主题：*Re: [Freesurfer] extracting mean thickness from specific cluster >> *收件人：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu> >> *抄送：* >> >> On 2/21/14 10:04 AM, charujing123 wrote: >>> Hi all, >>> I finished the mri_glmfit-sim, and got some clusters in the cluster >>> summary. >>> 1,I want to know how to extract mean thickness for each subject in >>> this cluster? >> >> There should already be a file there called something like >> something.y.ocn.dat. This will have a row for each subject and a >> column for each cluster. The value will be the mean for that subject >> inside that cluster. >> >>> 2,If I want to extract mean thickness of each subject according to a >>> uncorrected p value, i.e. 0.005, what should I do to perform it? >> >> What do you mean? Over all vertices that survive? Or for each all >> clusterwith a cluster-forming threshold of .005? If the latter, you >> can run mri_glmfit-sim with --cwp 1 --cache 2.3 abs >> >> >>> Thanks. >>> All the best. >>> Rujing Zha >>> 2014-02-21 >>> ------------------------------------------------------------------------ >>> >>> charujing123 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://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 > -- 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 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.
