Try using a seg instead of an annot, eg, -seg aparc+aseg.mgz 1007 for left fusiform
On 12/06/2017 12:13 PM, Ashley Cole wrote: > Hi, > > I was wondering if anyone could kindly help me on this matter. > > Thank you, > > Ashley > > On Wed, Nov 29, 2017 at 11:46 AM, Ashley Cole <coleashle...@gmail.com > <mailto:coleashle...@gmail.com>> wrote: > > 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 <mailto: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> > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > > > > > > _______________________________________________ > 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
