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

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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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