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Hi Freesurfers,
I am running the new Freesurfer 7.4.1 on Ubuntu 22.04, but ran into the
following error. I tested the same data using FS 6.0.0 and it worked fine.
The command I am using is recon-all -3T -all. Thanks.
mri_label2vol --defects
/qmi08_rai
09:36
> To: freesurfer@nmr.mgh.harvard.edu; Hoffmann, Malte,PhD
> Subject: Re: [Freesurfer] Use synthetic in recon-all pipeline
>
>
>
> On 5/28/2023 1:32 PM, Ruifeng Dong wrote:
>
> External Email - Use Caution
>
> Hi all,
>
> I am running freesurfer 7.3
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Dear all,
We acquired the images (sagittal, 176*256*256) with obliqueness, because we
tried to match the prescription with the subject's head positioning. Then,
the obliqueness is shown in the header of the image.
We used this image in recon-all. Afte
.png]
Best,
Ruifeng
On Tue, Jun 20, 2023 at 9:59 AM Douglas N. Greve
wrote:
> External Email - Use Caution
>
> This was done a long time ago to conserve space/memory. There is a
> rescaling that is done, so it should not affect the bias correction much
>
> On 6/14/2023 3:3
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Hi Yujing,
Thanks. I am wondering about the reason why Freesurfer converts data types
to uchar. Doesn't this affect the non-uniformity bias correction
that follows?
Best,
Ruifeng
On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing
wrote:
> Extern
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Hi all,
I am running freesurfer 7.3.2 for segmentation of T1 data. It seems like
still using the old skull stripping tools by default. How should we change
it to using synthstrip? (Question 1)
Also, is it a good idea to also turn on the --no-csf flag
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Dear Freesurfer community,
I wonder if Freesurfer uses any filter to deal with the noise in the image,
before segmentation. If so, is the filter spatially local or nonlocal?
Thanks.
Best,
Ruifeng
___
Freesu
*-1.77340899878395*
CC_Mid_Posterior 767 710.9 769 711.8 *0.126600084400053*
CC_Central 574 536.1 565 521.7 *-2.68606603245663*
CC_Mid_Anterior 621 579.5 629 576.1 *-0.58671268334771*
CC_Anterior 1110 1022.8 1107 1010.9 *-1.1634728197106*
On Tue, Aug 30, 2022 at 6:28 PM Ruifeng Dong wrote:
> Thanks for point
ere is not enough information to understand what you did in #2
>
> On 8/30/2022 3:56 PM, Ruifeng Dong wrote:
>
> External Email - Use Caution
> Hi all,
>
> I am computing volumetry using freesurfer using two different runs.
>
> 1. I just use recon-all -all, and th
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Hi all,
I am computing volumetry using freesurfer using two different runs.
1. I just use recon-all -all, and then look at the aseg.stats file.
2. I ran recon-all only to the 12th step where gca labeling is done. It
doesn't generate the aseg.mgz file
in a structure can change (e.g.
> is the fimbria part of the hippocampal label?)
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ruifeng Dong
> *Sent:* Tuesday, August 30, 2022 2:34 PM
> *To:* Free
t;
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ruifeng Dong
> *Sent:* Tuesday, August 30, 2022 11:07 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Segmentation protocol used by Freesur
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Is Freesurfer using Neuromorphometrics’ General Segmentation Protocol, or
something different?
What are the differences between different protocols?
Thanks!
Ruifeng
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