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> 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> 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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