[Freesurfer] Creating functional ROI

Dear FreeSurfer community, I am new to FreeSurfer and I apologize in advance if my questions are too naiive. I have some nii files for both a localizer and an experiment. I would like to find some ROIs in the localizer, get their coordinates, create a mask, and then find those regions on the expe

[Freesurfer] Creating functional ROI

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 se

Re: [Freesurfer] Creating functional ROI

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 > >

Re: [Freesurfer] Creating functional ROI

Hi Doug, Thank you for your response. 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: *"annotatio

Re: [Freesurfer] Creating functional ROI

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

Re: [Freesurfer] Creating functional ROI

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 wrote: > Hi Doug, > > > I ran the funcroi-config command the same way the tutorial suggested: > *"funcroi-config > -annot aparc fusiform -analysis eba-fba.native

Re: [Freesurfer] Creating functional ROI

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

Re: [Freesurfer] Creating functional ROI

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-c

Re: [Freesurfer] Creating functional ROI

I was wondering if there is other way than using matlab to do this. On Mon, Dec 11, 2017 at 9:07 PM, Ashley Cole wrote: > 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