Hi Ronny, On 03/20/2013 05:57 PM, preci...@nmr.mgh.harvard.edu wrote: > Hello all, > I am starting to run some analysis using fs-fast and I had a few basic > questions that I couldn't find answers on the wiki/tutorial. > > 1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat > What is the format of the input file for -tpexclude? Is it simply a single > column of integers representing the seconds that need to be excluded? My > example, my TR is 3 and I know I want to remove acquisitions 134 and 140 > because of motion. Do I simply need to have a file that has the following > content? > 402 > 403 > 404 > 420 > 421 > 422 This is correct, except that time starts at 0. So time point 1 = 0, tp2 = 3sec, etc. So tp134 = (134-1)*3 = 399, not 402 > > > 2) bold data - Resampling to "common space" > In the preprocessing step, the bold data is resampled to 76x76x93. My data > is 96x96x50. Does starting with data that is larger than the "common > space" cause a problem in the analysis? No > > 3) Viewing analysis for individual bold data runs > When the First level analysis is completed, the resulting files are a > combination of all of the bold data runs of the session. Is there a way to > make it so that I can also see the different activity for individual runs > within the session or does the analysis only do it by combining data for > all runs within a session? By default it combines all the runs. If you want to see what it looks like in each run, there are two things you can do. First, you can run selxavg3-sess with the -run-wise option. This causes it analyze each run separately. This the easy way. Second, you could recode your stimulus numbers to be run specific. This means you have to create a new analysis and specify new contrasts. doug > > Thanks in advance! > -Ronny > _______________________________________________ > 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 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.
