Ok. But when I view them using tksurfer, absolute contrast gives me both positive and negative contrast clusters. Even if I copy the csd files and change the header information, could I view just positive or negative significant clusters on tksurfer?
Many Thanks for your help Regards Koushik ________________________________________ From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, February 15, 2012 10:41 AM To: Govindarajan, Koushik Athreya Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] monte carlo simulation question In principal, it should be the same correction as for the positive as the simulation should be symmetrical across sign. But mechanically/programatically, I don't have an easy way to do it. You can copy the csd files to a new name and change the sign listed in the header. doug Govindarajan, Koushik Athreya wrote: > Many Thanks for that Doug. It worked great. I do have another question for > you about monte carlo simulation. Say I run a simulation with an absolute > contrast initially. After the analysis is done, if I need results for a > negative contrast, is there a way to do that after the simulation or does it > have to be a separate mri_glmfit-sim again? > > Thanks > Regards > Koushik > > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, February 15, 2012 10:09 AM > To: Govindarajan, Koushik Athreya > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] monte carlo simulation question > > Hi Koushik, download this file and copy it into the mri/transforms directory > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.xfm > Then rerun mri_glmfit-sim with the --no-sim option so that it picks up > where it left off. You will need to give the "csdbase" which you passed > it as the 4th argument to the --sim option. > > doug > > > Govindarajan, Koushik Athreya wrote: > >> Hello group, >> >> I am running the multiple comparisons simulation after my mri_glmfit >> finished. I see that it went through all the iterations and then quit with >> the following error message it could not find the talairach.xfm file in my >> average brain. I did not use the fsaverage and instead created my own >> template based on average normal brains. I went back and checked my average >> subject folder and indeed, there is no talairach.xfm file in there. I also >> see that the 'tmp' directory in there has a lot of the intermediate files. I >> do not recollect seeing an error message when I created my average brain. >> So, was not sure what was going on. My 2 questions are: >> >> 1. How can I finish the rest of the make_average_subject processing to >> create my talairach.xfm file? Do I have to start from scratch or can I >> continue from where it left off? >> >> 2. The same question with the mri_glmfit-sim analysis also. Is there a way >> for me to continue from where it left off using the new talairach.xfm file >> or do I have to start from scratch and go through so many hours of >> simulation again? >> >> Thanks a lot for all the help >> Koushik Govindarajan >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
