reesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, July 19, 2017 at 9:48 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] dmri_motion -T threshold
We want to match on dropout as well which would require us to cha
Sent: Wednesday, July 19, 2017 9:31 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dmri_motion -T threshold
If neither of your groups has bad slices (which you should confirm by looking
at the images), then they are matched in that respect. You can then check for
differences in the
>]
on behalf of Buckless, Colleen
[buckl...@kennedykrieger.org<mailto:buckl...@kennedykrieger.org>]
Sent: Friday, July 14, 2017 3:35 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] dmri_motion -T threshold
Hi All,
I've been using dmri_motion to quantify motion in our DTI
hanks,
Colleen
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, July 18, 2017 6:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dmri_motion -T threshold
Hi Colleen - Do the DWIs of your subjects
ut!
Best,
a.y
From: 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: [Freesurfer] dmr
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
Hi Ruth - It expects the output format of eddy_correct. It then computes
the transforms between consecutive frames from the transforms between each
frame and the reference frame.
Best,
a.y
On Sun, 29 Nov 2015, Ruth Carper wrote:
Hi,
I'm hoping to use the dmri_motion tool to quantify motio
Hi, I'm hoping to use the dmri_motion tool to quantify motion for some
diffusion data that did not use the eddy_correct tool. We have registration
matrices that we've successfully reformatted, but I've been scanning the
FreeSurfer forum and see some conflicting information about whether the inp
slices.
Ruth
From: Anastasia Yendiki
To: Ruth Carper
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Friday, March 14, 2014 4:46 PM
Subject: Re: [Freesurfer] dmri_motion
Hi Ruth - These parameters are described
floor values (0 and 1 respectively) for
the Benner score and % bad slices.
Ruth
From: Anastasia Yendiki
To: Ruth Carper
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Friday, March 14, 2014 4:46 PM
Subject: Re: [Freesurfer] dmri_motion
Hi Ru
Hi Ruth - These parameters are described in Benner 2011 (cited in our
paper). The -T threshold is mostly what you might need to change,
depending on your scanner. You should look at the low-b images and find a
rough lower threshold for the image intensities of brain voxels. It
doesn't have to
Hi,
I've been using dmri_motion to quantify motion in our DTI data. Can you give
any guidance on selecting values for the -D and -T flags? I didn't see
anything in the wiki or in your related papers and it can have a substantial
effect on the outputs.
Thanks.
Hi anastasia,
Thanks for your answer!
I've already find where is my bug.
I've downloaded other tracula update (Centos4). After I download Centos6,
tracula runs without problems with the files used before.
Thanks again
No dia 6 de Fev de 2014 00:56, "Anastasia Yendiki" <
ayend...@nmr.mgh.harvard.e
Hi Liliana - This error indicates that it could not find the
/home/lapsi/test/bvals file at all, not that the file had the wrong
format. Does that file exist?
Also, if you run "trac-all -prep -noqa", you're telling trac-all NOT to do
the QA step that calculates the motion measures, so I'm co
Hi,
Within the new Tracula update and with outputs resulted from *trac-all
-prep -noqa* I ran
*: *
*dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals'
--mat './dwi.ecclog'*
And an error message appears:
*machine x86_64Output motion measure file:
/home/lapsi/
15 matches
Mail list logo
