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> 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
greve@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.