Hi Doug,
I ran the funcroi-config command the same way the tutorial suggested: *"funcroi-config -annot aparc fusiform -analysis eba-fba.native.rh -contrast faces-vs-objects -thresh 2 -sign pos -roi rh.fus.test.roicfg -force"* However, I got this error: *"annotations can only be used with surface-based analyses"* I have done my mkanalysis-sess in the *native space*, i.e.: *"**mkanalysis-sess -fsd bold -stc odd -surface self rh -fwhm 5 -event-related -paradigm ..."* Do you think this is the problem? Meaning, the surface here should be fsaverage instead of self? And if yes, what if I need everything in the native space? Thank you, Ashley > > > On Mon, Nov 13, 2017 at 10:21 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Start with funcroi-config. Run it with -help to get documentation >> including several examples. Let me know if you still have questions >> >> >> On 11/11/2017 11:56 AM, Ashley Cole wrote: >> > Dear Doug/Bruce, >> > I appreciate any insights on this. >> > Thank you, >> > Ashely >> > >> > ------------------------------------ >> > >> > >> > I am new to FreeSurfer and I apologize in advance if my questions are >> > too naiive. >> > >> > My main goal is to keep everything in the native space. Also, I am >> > looking for percent signal change in selected ROIs. >> > >> > >> > First, I ran recon-all command. Then, I preprocessed the functional >> > data in native space. The command that I ran was: >> > >> > preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 >> > -fwhm 5 -per-session -force >> > >> > >> > >> > Then, I configured my analyses and contrasts in each hemisphere, as >> > well as the volume. >> > >> > Finally, I ran the analyses for each hemispheres and the volume. I ran >> > this command: >> > >> > >> > selxavg3-sess -s sess01 -analysis ffa.native.rh >> > >> > >> > >> > Lastly, I visualized the results by running these commands: >> > >> > tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c >> > faces-vs-bodies -self >> > >> > >> > >> > tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self >> > >> > >> > >> > So far, I think I have done everything correctly. I am seeing the >> > activation ROIs where I am supposed to. >> > >> > >> > >> > Now, I would like to be able to select these ROIs/clusters, take their >> > voxel coordinates/numbers and create a mask. (These are my localizer >> > nii files.) Then, use this mask on the main experiment (non localizer) >> > nii files and get the percent signal change in those selected voxels. >> > Is this possible? >> > >> > >> > I have found this tutorial >> > https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs >> > <https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs> but >> > unfortunately I am not following it. I don't see these options in >> > tksurfer. >> > >> > >> > Also is it possible to create an ROI on the surface? >> > >> > >> > I appreciate any help. >> > >> > >> > >> > Thank you so much >> > >> > >> > >> > Ashley Cole >> > >> > >> > >> > _______________________________________________ >> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> 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. >> >> >
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