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.
