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 [greve@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 [greve@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:
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?
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
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