Hello Doug, Thanks for your help on this. Ive run it again and there doesnt seem to be a problem. Its just that when I smooth it by 15 now the residual is about 23. When I ran it the other time, the residual was 47 for some unknown reason.
Regards, Joshua On Thu, Jun 6, 2013 at 10:14 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > I think when you smooth it that much strange things happen. Try just one > smoothing of 15mm. > > > > > On 06/06/2013 03:36 AM, Joshua deSouza wrote: > >> Hi Doug, >> >> I did not specify anything in the mris_preproc, so it would be using the >> unsmoothed data. I only specify smoothing during the mri_surf2surf, which >> is 15 and then run glmfit. So what could be the reasons why i'm getting a >> residual fwhm of 47? >> >> Regards, >> >> Joshua >> >> On Thu, Jun 6, 2013 at 12:16 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> Unless you specify otherwise, mris_preproc will use unsmoothed >> data. If you then smooth it with mri_surf2surf and run run >> mri_glmfit with --fwhm then you will be smoothing it twice. >> doug >> >> >> >> >> On 06/04/2013 09:49 PM, Joshua deSouza wrote: >> >> Hello Doug, >> >> Each individuals subject data has already been smoothed by 5 >> 10 15 20 and 25 through the qache function during the initial >> processing. >> >> I'm a little confused now. I thought that the mri_preproc >> would use the non-smoothed values of the subjects and create >> an mgh file. After which I smooth the mgh file and then use >> mri_glmfit to analyse it according to the contrasts. >> >> If the above is not the case and the subject data has already >> been smoothed, then what should I do if I wish my final mgh >> file to have a smoothing value of 15 before doing a glmfit on it? >> >> Thank you, >> >> Joshua >> >> >> On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza >> <desouzajoshu...@gmail.com >> <mailto:desouzajoshua00@gmail.**com<desouzajoshu...@gmail.com> >> > >> <mailto:desouzajoshua00@gmail.**com <desouzajoshu...@gmail.com> >> >> <mailto:desouzajoshua00@gmail.**com <desouzajoshu...@gmail.com>>>> >> wrote: >> >> Hello Doug, >> >> Each individuals subject data has already been smoothed by >> 5 10 15 >> 20 and 25 through the qache function during the initial >> processing. >> >> I'm a little confused now. I thought that the mri_preproc >> would >> use the non-smoothed values of the subjects and create an mgh >> file. After which I smooth the mgh file and then use >> mri_glmfit to >> analyse it according to the contrasts. >> >> If the above is not the case and the subject data has >> already been >> smoothed, then what should I do if I wish my final mgh file to >> have a smoothing value of 15 before doing a glmfit on it? >> >> Thank you, >> >> Joshua >> >> On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> Hi Joshua, when you add --fwhm 15 to the command line >> you are >> instructing mri_glmfit to smooth by 15mm. Is this what you >> want? Or is the data already smoothed? >> doug >> >> >> >> On 6/3/13 12:26 AM, Joshua deSouza wrote: >> >> Hi Doug, >> >> The command line is mri_glmfit --y lh.t.15.mgh >> --fsgd t.txt >> dods --C t1.txt --surface fsaverage lh --cortex >> --fwhm 15 >> --glmdir lh.t.15.glmdir >> >> I am doing a whole hemisphere analysis and am >> measuring >> cortical thickness. I do not have my own mask but >> I have >> doubts about the mask that has been produced >> because from >> previous studies, there has been significant >> thinning in the >> area around the hippocampus and parts of it are >> being left >> out in the mask, such as the para-hippocampal region. >> >> Regards >> >> Joshua >> >> On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> The residual FWHM is measured from the data >> itself. You >> apply a certain amount of smoothing, but there >> is already >> some smoothness to the data, so the final fwhm >> is a >> combination of what is already there and what >> you apply. >> A fwhm of 47 is huge and may indicate that >> something is >> wrong. What is the input? cortical thickness? >> Are you >> using your own mask or is this a whole >> hemisphere analysis? >> >> doug >> >> >> >> >> >> >> On 6/2/13 10:29 PM, Joshua deSouza wrote: >> >> Hello Doug, >> >> Thank you for your quick replies to my >> queries. Really >> appreciate it. >> >> I have found the files containing the >> cortical thickness >> values. Thank you. I assume that the order >> in which they >> follow are based on the fsgd file and the >> cluster >> annotation numbers. >> >> I was just slightly confused about the >> residual fwhm. I >> have already done a smoothing of 15 on the >> file and have >> recieved a residual value of 47, which I >> assume is >> extremely large. Since I'm finding out >> values for the >> entire cortex I cannot do a glmfit-sim as >> there are no >> fwhm cache values of 47. Could you please >> tell me what >> the residual values mean? What do you >> recommend I do? >> Is there anything I can read up on to find >> out more >> about this? (Please pardon my questions if >> they seem a >> little trivial) >> >> Thank you >> >> Joshua >> >> On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> This file is always created by >> mri_glmfit-sim. It >> might be named something different >> depending on your >> parameters (should always end in >> y.ocn.dat) >> doug >> >> >> On 6/2/13 3:57 AM, Joshua deSouza wrote: >> >> Hi Doug, >> >> This file that your saying, will >> be created after >> glmfit-sim is done using the cache >> function and a >> threshold of 1.3 and absolute >> ,with y being the >> fsgd file? Am I understanding this >> correctly? >> >> Thank you >> >> Joshua >> >> On Sat, Jun 1, 2013 at 12:14 AM, >> Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> There should be a file called >> something like >> cache.th13.abs.y.ocn.dat. >> This will have a column for >> each cluster and a >> row for each subject. The >> value in the row will be the >> input for each >> subject. >> doug >> >> On 05/30/2013 11:21 PM, Joshua >> deSouza wrote: >> > Hello everyone, >> > >> > Please pardon my rather >> simple question >> > >> > I have done a GLM fit >> anlysis and have >> obtained a file sig.mgh alonf >> > with a few others after the >> analysis.As I >> know, I do not have to >> > create ROIs in order to do >> this. I also >> understand that doing a >> > multiple comparison analysis >> just compares >> the regions of importance >> > and evaluates them giving >> the most resilient >> cluster depending on the >> > threshold. So, this does not >> give a thickness >> estimate. I would like >> > to know how do I get the >> cortical thickness >> values from the results? >> > If so, can I do it after glmfit? >> > >> > And thanks Doug for your >> help in the other >> questions that I had prior >> > to this! >> > >> > Thank you >> > >> > >> > >> ______________________________**_________________ >> > Freesurfer mailing list >> > >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> <mailto: >> freesur...@nmr.mgh.**harvard.edu <Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/* >> *freesurfer<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<gr...@nmr.mgh.harvard.edu> >> > >> <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<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 <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<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> >> > >> < >> 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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> <mailto: >> freesur...@nmr.mgh.**harvard.edu <Freesurfer@nmr.mgh.harvard.edu> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/* >> *freesurfer<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<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. >> >> >> >> >> >> >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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