[Freesurfer] Fwd: Cortical thickness from ROI in volume format

-- Forwarded message -- From: Martin Juneja Date: Tue, Jan 31, 2017 at 4:38 PM Subject: Cortical thickness from ROI in volume format To: Freesurfer support list Hi FreeSurfer experts, My goal is to extract cortical thickness

Re: [Freesurfer] flip4fsl missing in stable6

Hi Qiuyun - You can use orientLAS instead. Hope this helps, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fan, Qiuyun [qiuyun@mgh.harvard.edu] Sent: Tuesday, January 31, 2017 6:03 PM To:

Re: [Freesurfer] flip4fsl missing in stable6

Hello Qiuyun, What command did you call that complained about this? And what was the error exactly? On 01/31/2017 06:03 PM, Fan, Qiuyun wrote: > Hi FreeSurfer experts, > > > > I figured 'flip4fsl' is missing from > /usr/local/freesurfer/stable6/bin/. Can someone help to make a copy > from

[Freesurfer] flip4fsl missing in stable6

Hi FreeSurfer experts, I figured 'flip4fsl' is missing from /usr/local/freesurfer/stable6/bin/. Can someone help to make a copy from /usr/local/freesurfer/stable5_3_0/bin/flip4fsl, if possible? Thanks a lot! Best, Qiuyun ___ Freesurfer mailing

Re: [Freesurfer] Neighborhood thickness in a 10mm radius

Douglas, thank you for the quick reply. I am trying to figure out how can mri_fwhm help in this contect but can't grasp it. I tried some of the example commands in the wiki, applied on a XX.thickness file, but the outcome is NaN. To clarify, what I am trying to do is detect local variations in

Re: [Freesurfer] Neighborhood thickness in a 10mm radius

You can smooth it. This would give you a gaussian kernel instead of the box kernel that you describe. Set the fwhm to the radius you want (mris_fwhm with --smoothonly option) On 01/31/2017 04:48 PM, Dorian P. wrote: > Hi Freesurfers, > > Thank you for the help you provide through this list. >

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

Hello, I'm reposting the following just in case anyone has any ideas. Any input would be greatly appreciated! Thank you very much for the suggestion. Here then are my attempts at putting what you said into two sequential commands: mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \

[Freesurfer] Binary images multiplication

Hi, I would like to multiply two binary images (standard brain image with an ROI) using fslmaths (or may be using some other way) command. Although both are in standard space but image dimensions are different. I was wondering if there is any way I can do that without any co-registration step.

Re: [Freesurfer] longitudinal tracula error

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files are generated, then you’re good to go. Bedpost does not differentiate between longitudinal and cross-sectional data, so it’s run separately on each time point’s …/dmri/ folder. Best, a.y From:

[Freesurfer] Postdoctoral Position in Division of Neurotherapeutics at MGH/HMS (Boston, MA)

Hi everyone, The Division of Neurotherapeutics at Massachusetts General Hospital (Boston, MA) has an open postdoctoral position. The posting is below: NEUROIMAGING POSTDOCTORAL POSITION IN DIVISION OF NEUROTHERAPEUTICS AT HARVARD MEDICAL SCHOOL/ MASSACHUSETTS GENERAL HOSPITAL The Division