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Thanks Bruce.
Doug, can I get your advice on this? As I say, I currently do the following to
get to native surface:
bbregister to register the native functional volume data to the T1
* bbregister --s sub-0006 --feat
/media/HDD/ICA_SSD_files/Gro
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Dear all,
I want to run recon-all with the -nofix command, so that no fix of the topology
is done, because it takes too much time or never finishes.
Especially these commands in the recon-all.log file never finish.
PIDs (232383 232386)…
But sometime
No, not yet. FLAIR itself would probably not be for this anyway as it
usually does not have good gray/white contrast
On 4/19/2021 10:00 AM, Jindal, Saurabh wrote:
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Hi experts,
Could we analyze FLAIR images using freesu
There is nothing more you need to do. With --etiv, asegstats2table will
divide by the eTIV (and multiply by something like 100k to make the
values reasonable). At that point it is corrected. You could also
regress against eTIV rather than dividing by it. I don't know which one
is better.
On 4
can you send the bbr log file?
On 4/19/2021 2:29 PM, Russo, Andrew William wrote:
Hello FreeSurfer Developers,
I am registering FA maps to T1 for a group of subjects with MS and in
many cases the registration is poor for the anterior corpus callosum
(attached), cerebellum, pons, and temporal
and do they each have a norm.mgz?
On 4/19/2021 4:11 PM, Zeng, Qi wrote:
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Hi Douglas,
I found the aseg.presurf.mgz for all cross sessions and base using
version 6.0.
Best,
Qi
On Sun, Apr 18, 2021 at 10:43 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.ed
It looks like you made some manual edits, then re-ran recon-all, but did
not do so fully (eg, used autorecon2 but not autorecon3). Does this make
sense?
On 4/20/2021 4:35 AM, 林鈺庭 wrote:
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Dear FreeSurfer Developers:
We analyzed MRI T1 image data on freesur
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Hi Douglas,
They each contained mri/norm.mgz.
Best,
Qi
On Tue, Apr 20, 2021 at 10:10 AM Douglas N. Greve
wrote:
> and do they each have a norm.mgz?
>
> On 4/19/2021 4:11 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
Log file is attached.
Thank you,
Andrew
Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N.
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Hi there,
Still wondering if we can get some help with this. Our update is the following:
1. When we run make_average_subject with some chimp scans, with default
settings, it runs but the average surfaces are inflated compared to the
individual
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Thank you so much.
Saurabh
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Tuesday, April 20, 2021 9:04 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FLAIR image
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it seems that
there is some non-hippocampal inclusion in the form of choroid plexus and
adjacent peri-ventricular white matter. Do we have a standard cutoff criterion
for
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Hi Eugenio,
This is recon-all (aseg.mgz), and not the subfields. Thanks
Saurabh
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Sent: Tuesday, April 20, 2021 10:36 AM
To: Freesu
Hi Stephan
I think there has always been topology fixing. The ?h.orig should be created
prior to the fixing then corrected I believe, but if you have big topological
defects you probably want to figure out why and correct them. Have you
visualize the ?h.inflated.nofix or the ?h.orig.nofix? If t
Dear Saurabh,
Is this recon-all (aseg.mgz), or the hippocampal subfield module?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Jindal, Saurabh"
Reply-To: Freesurfer support list
Date: Tuesday
If you’re only/mostly interested in the hippocampus, I’d encourage you to try
the subfield module 😉
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of "Jindal, Saurabh"
Reply-To: Freesurfer support list
Date: Tue
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Okay, so could I expect better segmentation results from that without having
adjacent choroid plexus/white matter included as hippocampus.
Saurabh
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Go
Hard to tell without seeing your data, but it is sometimes the case. You could
try running the module on a couple of your worst cases and see what happens. It
takes about 30 minutes per case.
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesia
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Okay, will do that. Do we have a criteria/cut-off for hippocampal inclusion?
Like how many non-hippocampal voxels included as hippocampus are okay to pass?
And if we don't then could you suggest me on how to go about it? Thanks!
Saurabh
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That worked.
Thank you,
Christina
Am 16.04.2021 um 19:47 schrieb Hoopes, Andrew:
Hi Christina,
You’ll need to specify the version tag. You can try:
docker pull freesurfer/freesurfer:7.1.1
best,
Andrew
*From: *freesurfer-boun...@nmr.mgh.harvard.
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Dear FS experts,
Hope this finds you well.
I would like to check whether the following the correct approach for my models
in glm_fit. I am testing whether gait speed is associated with cortical
thickness, adjusting for 4 covariates (sex, age, bmi, an
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Hi Bruce,
I tried your suggestion, and it worked perfectly. Thank you so much!
Best,
Caroline
--
(Caroline) Xueying Ren
Graduate Student
Department of Psychology
University of Pittsburgh
she/her/hers
x...@pitt.edu
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