Oh, yes, I was thinking you were starting at 1 not 0. Sorry about that. doug
On 03/21/2013 12:45 PM, preciado@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, preciado@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.
- 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
- 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
- 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
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