[Freesurfer] How to convert surface-based atlas to annotation?

External Email - Use Caution Dear FreeSurfer Developers, To analyze functional connectivity, I first got Shen 268 surface-based atlas from Neurovault. Now I want to extract average time series data from my subjects based on the atlas but I have no idea how to make annotation.

Re: [Freesurfer] How to convert surface-based atlas to annotation?

if mris_convert supports it. I’m curious how you got the .gii files. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andy Kim Sent: Thursday, January 5, 2023 3:05 AM To: freesurfer Subject: [Freesurfer] How to convert surface-based atlas to annotation? Exte

Re: [Freesurfer] How to convert surface-based atlas to annotation?

let me know your mris_convert command line? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andy Kim Sent: Thursday, January 5, 2023 9:15 PM To: Freesurfer support list Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation? External

Re: [Freesurfer] How to convert surface-based atlas to annotation?

d you mind letting me know how you created rh.shen.atlas.1.label? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andy Kim Sent: Sunday, January 8, 2023 1:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] How to convert surface-based atlas to

Re: [Freesurfer] How to convert surface-based atlas to annotation?

., or it will fail argument check. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andy Kim Sent: Monday, January 9, 2023 8:25 PM To: Freesurfer support list Subject: Re: [Freesurfer] How to convert surface-based atlas to annotation? External Email

[Freesurfer] Do you have a specific reason for having only 3 motion regressors for connectivity analysis?

External Email - Use Caution Dear FreeSurfer Developers, I am trying to analyze functional connectivity using Freesurfer. When I checked FSFAST tutorial, it says: Sample command: "mkanalysis-sess -analysis fsrest.surf.lh -surface self lh -fwhm 5 -notask -nuisreg vcsf.dat 1 -nuis

[Freesurfer] How to get individual betas (parameter estimates) in certain ROI?

External Email - Use Caution Dear FreeSurfer Developers, Hi. Thanks to FreeSurfer, I finished a group activation analysis with FS-FAST. Now I want to draw a ROC curve to check how well my task conditions can distinguish M1 and S1. (M1 is more activated under certain condition of

[Freesurfer] Which motion correction parameters are used in FSFAST?

External Email - Use Caution Dear FreeSurfer Developer, Hi. Thanks to FreeSurfer, I could perform surface-based activation analysis with FSFAST. Now I want to do surface-based functional connectivity analysis. For the sake of consistency, I want to use the same nuisance regresso

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

what you want, then include -mcextreg On 3/29/2023 11:29 PM, Andy Kim wrote: External Email - Use Caution Dear Douglas N. Greve, My experiment design is block design with 2 conditions. Here is the mkanalysis command line: mkanalysis-sess -fsd main -stc siemens \ -surface fsaverage lh -f

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

re in the .mcdat file On 3/30/2023 11:39 PM, Andy Kim wrote: External Email - Use Caution Dear Douglas N. Greve, Thank you. I followed your advice and re-ran the codes with -mcextreg. Now there are 3 more columns in X.mat for each run. I assume those 3 additional columns are m

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Which motion correction parameters are used in FSFAST? The regressors have been demeaned; other than that, they should be the same. On 3/31/2023 6:59 PM, Andy Kim wrote: External Email - Use Caution Dear Douglas N. Greve, But the 3 additional columns

[Freesurfer] How to create a functional ROI on surface where activation is peak?

External Email - Use Caution Dear FreeSurfer developers, Hi. I've always appreciated your help. I am writing this email to kindly ask you how to create a functional ROI where activation (which is a result of FS-FAST) is peak. In volume-based analysis, people often make a "3mm-s

Re: [Freesurfer] How to create a functional ROI on surface where activation is peak?

--s fsaverage --hemi lh mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh delta.sm3.bin.mgh will be a binary disk approximately 3mm in radius On 4/4/2023 7:24 AM, Andy Kim wrote: External Email - Use Caution Dear FreeSurfer developers, Hi. I've always appreciated your

[Freesurfer] How can I increase radius of a binary disk?

External Email - Use Caution Dear Dr. Douglas N. Greve, Thanks to you, I could have a binary disk approximately 3mm in radius by the codes you told me (https://secure-web.cisco.com/1z0F3-vP1KDJI6B_AsTyKAaKNmMd0vO7tGkwv_YiAe4mgtFL1QdTiYs_dYZa0SNYmBNh1h2ge_bd6h98_TjHFMZx8lfVf63LrK

Re: [Freesurfer] How can I increase radius of a binary disk?

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How can I increase radius of a binary disk? External Email - Use Caution oh, you should have used --fwhm 3 on that first command, and if you want 5mm then use --fwhm 5 On 5/19/2023 7:15 AM, Andy Kim wrote: External Email - Use Caution Dear

[Freesurfer] Can I use Freeview (tksurferfv) Tools on surface?

External Email - Use Caution Dear FreeSurfer Developers, Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D8qAugBQR0S6zkInLYQn1Xl3TOY0oJFkbI6RPoALU