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I'm not sure how to remove those edge effects. My guess is that they are motion artifacts (eventhough you are using motion correction regressors). Does the activation otherwise look ok given your task? I suppose you could just remove those slides by hand with mri_convert --cutends ...
On 8/16/2023 1:41 AM, Itzik Norman wrote:
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Dear FreeSurfer team,
I'm using fsfast to analyze 1.2mm^3 7T BOLD data collected with a partial coverage over the hippocampus and superior temporal lobe.
I ran preprocessing with the following flags: preproc-sess -d /functional-data -s SUB01 -fsd bold -surface SUB01 lhrh -fwhm 2 -init-header -bbr-int /functional-data/SUB04/bold mT2_WB -per-session
And then I ran the GLM analysis (stimulus-vs-baseline) using selxavg3-sess, keeping the data in the subject's native space (using the '-native' flag combined with '-per-session').
The resulting t-map shows a diagonal line of spurious activation along the edge of the functional volume. Is there a way to eliminate this artifact? (see figures attached)
Moreover, is there a way to use the -native flag together with -per-run? I want to simultaneously measure the hippocampal activation (in native space) and cortical activity smoothed on the surface; but I want all the data to be processed the same way (-per-run), and currently the volume analysis forces me to use -per-session.
I haven't encountered any previously documented issues similar to this one. Please let me know if you have any thoughts.
- FreeSurfer build stamp: freesurfer-darwin-macOS-7.3.2-20220804-6354275
- Platform: Mac Studio M1 (macOS)
- selxavg3-sess log: attached
- analysis config file: attached
Thanks, Itzik
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