Thank you, Doug. This worked. Now I have two questions:
1- Is it possible for a given threshold in funcroi-config to have let say 15 voxels on the surface but zero voxels in the volume? When I load the .sig map, I can see activation for a given threshold on the volume but when I run the funcroi-config and funcroi-sess, I get zero voxels. However, it returns non zero voxels for the surface. 2- Now that I have configured my functional ROIs on my localizer data, how can I find the percent change signal within that ROI for my experiment data (non-localizer session)? Sorry for my naiive questions. Best, Ashley On Wed, Dec 6, 2017 at 3:02 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 >
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