Hi there FreeSurfers,

I was thinking about using a propensity matched control sample for a study I am conducting that includes FS data. I would want to match each patient (i.e., MCI) with a specific control (re-using some controls multiple time(s) using the propensity matching, and then using paired sample statistics.

However, when looking on FS about qdec and group analyses using the command stream, I didn't see any information about if/how to set up a paired sample. Is it possible to do a matched paired sample (reusing control pts) with FS? If so, where I could get more information on it?

Thank you, Jacquie

Jacquelynn N. Copeland, M.A. Doctoral Candidate Medical/Clinical Psychology Program Department of Psychology University of Alabama at Birmingham Email:jcopeland@uab.edu ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of freesurfer-request@nmr.mgh.harvard.edu [freesurfer-request@nmr.mgh.harvard.edu] Sent: Tuesday, March 06, 2012 11:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 97, Issue 8

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Today's Topics:

1. controls points in 5.1 (Chris Hyatt) 2. mri_vol2surf error writing to nifti volume (Tina Jeon) 3. mri_cvs_register on a 64-bit Mac crash PETSC ERROR (Rey Ramirez) 4. (no subject) (Ryan) 5. overlaying sig.mgh onto normalized individual brains (Catherine Wan) 6. Re: (no subject) (Bruce Fischl) 7. Ask question about QAtools (chenchunhuichina) 8. Re: pwd: permission denied (Marcel Zwiers) 9. Re: mri_cvs_register on a 64-bit Mac crash PETSC ERROR (Bruce Fischl) 10. about QAtools (chenchunhuichina) 11. About recon-all (bowang21@mail.ustc.edu.cn) 12. Re: About recon-all (Bruce Fischl) 13. Research scientist in MRI imaging ? three-year contract available immediately (Fr?d?ric Andersson) 14. Re: about QAtools (Louis Nicholas Vinke) 15. PhD / Post-Doctoral position ? Neuroimaging of language and audition, University of Geneva (Narly GOLESTANI)

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Message: 1 Date: Mon, 05 Mar 2012 16:48:24 -0500 From: "Chris Hyatt" Chyatt@harthosp.org Subject: [Freesurfer] controls points in 5.1 To: freesurfer@nmr.mgh.harvard.edu Message-ID: 4F54EE580200002D0002B061@gwmail1.harthosp.org Content-Type: text/plain; charset=US-ASCII

Bruce,

You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag.

I too had noticed very different behavior after adding control points in v5.0 and v5.1, as many more regions were tagged as white matter in v5.1 than in v5.0.

Would anyone know if this flag exists and how to use it?

Thanks, Chris

Re: [Freesurfer] control point guidanceBruce Fischl Fri, 27 Jan 2012 11:58:38 -0800

Hi Mikeit's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect.Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know.Bruce

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Message: 2 Date: Mon, 5 Mar 2012 21:55:38 +0000 From: Tina Jeon Tina.Jeon@utsouthwestern.edu Subject: [Freesurfer] mri_vol2surf error writing to nifti volume To: "Freesurfer@nmr.mgh.harvard.edu" Freesurfer@nmr.mgh.harvard.edu Message-ID: C567682DBD3D104CA75A281451264BA301E4B5FC@swmsmailstu.swmed.org Content-Type: text/plain; charset="us-ascii"

Hi Freesurfers,

I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh

I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue?

Thanks all help appreciated,

Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center

Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event)

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