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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
