Thanks, Kevin So, I guess there is nothing special about retinotopy data, but the functionl overlay that I got doesn't look right. (not much activation)
Here is the two steps that I've done for the functional data before I overlay it onto anatomical data. Any comments are appreciated.
1. use "mricro" to turn functional data into Analyze format (*.img and *.hdr). 2. use "mri_convert" to turn the Analyze format data into *.bfloat to use them in functional overlay.
I guess that something is missing. That is I did not include anything about the experimental design, e.g., 1 2 1 2 1 2, or 1 2 3 4 1 2 3 4, etc. Where do I include such information in the analysis? I know where I put the design info in FSL, but not here in Freesurfer?
Nam.
Thanks, Kevin So, I guess there is nothing special about retinotopy data, but the functionl overlay that I got doesn't look right. (not much activation)
Have you tried playing with the thresholds, in the View->Configure->Functional Overlay dialog? I'm not sure if they will be set up properly for your data.
I guess that something is missing. That is I did not include anything about the experimental design, e.g., 1 2 1 2 1 2, or 1 2 3 4 1 2 3 4, etc. Where do I include such information in the analysis? I know where I put the design info in FSL, but not here in Freesurfer?
You'll have to bounce that question back to the freesurfer list, as that isn't something I work on at all. Sorry!
On Wed, 17 Nov 2004, Joongnam Yang wrote:
Thanks, Kevin So, I guess there is nothing special about retinotopy data, but the functionl overlay that I got doesn't look right. (not much activation)
Here is the two steps that I've done for the functional data before I overlay it onto anatomical data. Any comments are appreciated.
- use "mricro" to turn functional data into Analyze format (*.img and
*.hdr). 2. use "mri_convert" to turn the Analyze format data into *.bfloat to use them in functional overlay.
I guess that something is missing. That is I did not include anything about the experimental design, e.g., 1 2 1 2 1 2, or 1 2 3 4 1 2 3 4, etc. Where do I include such information in the analysis? I know where I put the design info in FSL, but not here in Freesurfer?
What do you want to do with them? Most people who use FreeSurfer analyze their functional data in SPM, FSL, AFNI, FSFAST and then map their results to the surface.
doug
Nam. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hello, i was running the stxgrinder-sess command and in the fsfast tutorial manual the results of this command are supposed to be f, fsig, t, sig, minsig, and iminsig. i don't get any t or sig files, and noticed that bert's tutorial data does not have these either. are these files not used anymore? also, does anyone know if where i can find the fsfast manual, not just the tutorial manual? thanks, margaret duff
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Joongnam Yang -
Kevin Teich -
Margaret Duff