Hi Julie,
Sorry for the late response. You will need to pass -bv (big ventricles) flag to
cross, base, and long processes.
Best,
Yujing
From: Julie Ottoy
Sent: Tuesday, November 15, 2022 11:56 AM
To: Huang, Yujing
Cc: Freesurfer support list ; fsbuild
Subject: Re: [Freesurfer] Fwd: Longitu
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Dear experts:
I have a doubt about finding the medial wall mask of a subject.
Would this be ok?
mri_label2label --srclabel lh.cortex.label --trglabel lh.cortex.label --outmask
lh.cortex.mask.nii.gz --regmethod surface --hemi lh --srcsubject 25633
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Dear Freesurfer team,
My colleagues and I performed a general linear model with FreeSurfer mri_glmfit
for whole brain analysis in intergroup comparison (g2v1) with a Monte-Carlo
correction.
I'd like to get the effect size of the analysis and I was
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Hi all, I just want to follow up with this email since it has been a while with
no replies. Thanks
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: Zeng, Victor (BIDMC - Keshavan - Psychiatry)
Se
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Dear experts,
I am trying to use freesurfer with a set of high-resolution images (0.6mm3
isotropic) and I found the brain mask generated by freesurfer is not ideal.
In this case, is it possible to supply a mask to recon-all? I've seen in
previous com
Hi Andrew,
1. The recon-all output is in the subject's native space.
2. So, registration of the volume (MNI) and surfaces (fsaverage) happens as
part of the recon-all process, but they're not resampled automatically i.e.
kept in the subject's native space. You can use mri_vol2vol command
It only applies to the volume calculation. You can use mri_gtmpvc
(search for PETsurfer -- applies to more than PET)
On 11/16/2022 11:00 PM, Julie Ottoy wrote:
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Hello FS team,
If I want to calculate the average diffusion-weighted signal from a
DWI image w
I don't know what version of FS you are using, but try adding --no-surfs
to the tkregisterfv command line
On 11/16/2022 8:46 PM, Peter J. Kohler wrote:
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Hello Freesurfer,
I am trying to run recon-all on a dataset, and a subset of appear to have
problems w
sorry, you did not include the previous emails so I'm not sure what you
are referring to. Also, please remember to post to the list. thanks!
On 11/16/2022 6:12 PM, Akansha Mahesh Naraindas wrote:
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>
> Thanks for your response,
>
> Yes the data is already in
I think it would be ok
On 11/16/2022 5:04 PM, Boa Sorte Silva, Narlon wrote:
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Would it be problematic if N4BiasFieldCorrection were to be applied to
the T1w before processing it in the standard recon-all pipeline?
The reason is because we wan
No, it does not matter.
On 11/16/2022 2:33 PM, Julie Ottoy wrote:
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Hi FS team,
I just wanted to double check if, for the longitudinal pipeline, it
matters which time point is being read first? For example, in the
command below, should -tp -tp in the ord
Sometimes the stroke will mess up the analysis in the undamaged hemi. A
lot of times people will make a mask of the stroke area, left-right
reverse the brain and register it to itself, then map the contralateral
hemi into the voxels of the stroke, then run recon-all on this modified
image.
On
register your diffusion data to the anatomical (bbregister), then map
the diffusion metric into the anatomical space (mri_vol2vol), then
compute the average over the regions you are interested in (eg,
mri_segstats --i diff.mgz --seg aparc+aseg.mgz --ctab-default --sum sum.dat)
On 11/3/2022 1:2
I don't remember what contrasurfreg output was. Can you elaborate?
On 11/9/2022 1:07 PM, Francois Tadel, Mr [Affiliate] wrote:
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>
> Hi Douglas,
>
> If I want to obtain outputs similar to -contrasurfreg, is it correct to
> execute the following commands?
>
> s
no, we don't have such a pipeline
On 11/9/2022 11:39 AM, AJ wrote:
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Hi,
Is there a specific pipeline for segmenting the cerebellum, cortical
gray and deep nuclei? Like the one for hippocampus and thalamus?
Best
___
I don't think the results are going to be that different. If you upgrade
to 7.3.2, you can run it on top of your v6 output (after making a
backup) and it should notice and keep your edits.
On 10/27/2022 2:16 PM, Rubenstein, Samantha Leigh wrote:
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Hi,
Our
Can you send the command line you used and the terminal output?
On 10/25/2022 8:19 PM, Paulk, Angelique C.,PhD wrote:
Hello,
I have yet another, likely obvious, question and I apologize if this
is answered elsewhere. I ran the below series of functions to apply
the HCP-MM1 (Glasser) atlas to t
try this
mri_segstats --seg lh.SignificantAreaOfROI.sig.mgh --i lh.w-g.pct.mgh
--id 1 --sum sum.dat
On 11/3/2022 2:08 PM, Fulton, Travis wrote:
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Hello FreeSurfer Developers,
I am trying to extract gray/white contrast stats for a specific area
within a co
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Hello Justina,
The error message you list is from VMware and not from Virtualbox. Those
are 2 different virtualization applications which expect the Linux operating
system virtual machine disk image file to be in different formats. As
far as I kno
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Dear FreeSurfer team,
Could you please provide me with the developer password (version 7.2.0)
to open the image?
Thank you!,
Diana
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