Re: [Freesurfer] dmri_motion -T threshold

2017-07-19 Thread Buckless, Colleen
rotational and translational motion to see if any further matching is needed. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Buckless, Colleen" mailto:buckl...@kennedykrieger.org>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>&

Re: [Freesurfer] dmri_motion -T threshold

2017-07-19 Thread Buckless, Colleen
om: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Buckless, Colleen [buckl...@kennedykrieger.org] Sent: Friday, July 14, 2017 3:35 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesur

[Freesurfer] dmri_motion -T threshold

2017-07-14 Thread Buckless, Colleen
Hi All, I've been using dmri_motion to quantify motion in our DTI data. We are uncertain how to determine what the -T threshold should be. We have read through the wiki and the related papers and are confused what this number represents, how it effects the output, and the rational for selecting

Re: [Freesurfer] error message while using autorecon1

2017-07-05 Thread Buckless, Colleen
rrect"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS? Thanks, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Sent: Wednesday, July 05, 2017 1:36 PM To: 'freesurf

Re: [Freesurfer] error message while using autorecon1

2017-07-05 Thread Buckless, Colleen
27;t sourced. Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the new

[Freesurfer] error message while using autorecon1

2017-07-05 Thread Buckless, Colleen
Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Cent

[Freesurfer] TRACULA: Motion measures only

2017-06-16 Thread Buckless, Colleen
Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless -