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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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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.
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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
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
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
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
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 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
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
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
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
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
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 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
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
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
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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
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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 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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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
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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