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 greve@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 <coleashley00@gmail.com mailto:coleashley00@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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>
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