Oh, yes, I was thinking you were starting at 1 not 0. Sorry about that. doug
On 03/21/2013 12:45 PM, preci...@nmr.mgh.harvard.edu wrote: > So, to clarify I got the number of the acquisitions that I want to exclude > from an fs-fast output file: fmcpr.dat in .../project/session/bold/008/ > > This file starts with scan number 0. So if > Scan 0 is seconds 0, 1, 2 > Scan 1 is seconds 3, 4, 5 > ..... > Shouldn't then; > Scan 134 be 402, 403, 404 > > > -Ronny > > >> 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 >> >> >> > -- 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.
