FreeSurfer does not segment extracerebral CSF. You can use samseg
(samseg --i orig.mgz --o samseg) and look at the samseg/seg.mgz file
On 12/13/2022 1:46 AM, priya padma wrote:
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Dear Team,
I have tried creating binary CSF mask from
# CSF:
# - 4: Left-La
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Dear Team,
I have tried creating binary CSF mask from
# CSF:
# - 4: Left-Lateral-Ventricle
# - 14: 3rd-Ventricle
# - 43: Right-Lateral-Ventricle
but I would like to know whether is it possible for us to get outer
CSF similar to fastsurfer.
An
that or see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 7/15/2019 9:39 AM, Bruce Fischl wrote:
you can do this with mri_convert:
mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz
cheers
Bruce
On Mon, 15 Jul 2019, Laboratorio de Neurocie
you can do this with mri_convert:
mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz
cheers
Bruce
On Mon, 15 Jul
2019, Laboratorio de
Neurociencia Funcional wrote:
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Thank you, Doug. The voxel resolution of the apa
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Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3.
Would it be possible to obtain the same file but with the native resolution?
Best,
Jose
El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escr
You can try running gtmseg. You will not want its final output, but along the
way it will produce a file called apas+head.mgz, and this will have a
semi-good segmentation of extracerebral CSF.
On 7/12/2019 12:14 PM, Laboratorio de Neurociencia Funcional wrote:
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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached file)? I would need
that the CSF mask contains not only the cerebral ventricles but also
the extracerebral CSF
No, not currently (next version)
On 6/6/2019 12:57 PM, Marina Fernández wrote:
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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?
Thank you in advance.
Best regard
Hi Marina
not with our default tools. Koen (ccd) has something that will generate
this, but it is not run by default.
cheers
Bruce
On Thu, 6 Jun 2019, Marina Fernández wrote:
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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Fr
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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?
Thank you in advance.
Best regards,
Marina.
___
Freesurfer mai
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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?
Thank you in advance.
Best regards,
Marina.
___
Freesurfer mai
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Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Freesurfer similar to that
obtained with the SPM segmentation (see attached)?
Thank you in advance.
Best regards,
Marina.
___
Freesurfer mai
If you just use 24, then you will see a small patch near cerebellum. The
257 is not part of the analysis yet. All the others are venticular
On 11/26/17 3:40 PM, Sam D wrote:
THanks for the response, Doug! So just to clarify, when I use
mri_binarize with the 24 label, which indicates CSF, I sho
THanks for the response, Doug! So just to clarify, when I use mri_binarize
with the 24 label, which indicates CSF, I shouldn’t expect to see any CSF
in my mask other than that within ventricles? The reason I ask is I’m
trying to generate the mask from which to acquire my csf regressor. Would
you in
We do not currently segment extra cerebral CSF. We will have this
segmentation in the next version.
On 11/21/17 9:00 AM, Sam D wrote:
Hello again FS experts,
Has anyone encounter this issue with FS CSF masks I described below?
I’ve reposted the issue here. I appreciate the help!
I am attem
Hello again FS experts,
Has anyone encounter this issue with FS CSF masks I described below? I’ve
reposted the issue here. I appreciate the help!
I am attempting to generate a CSF mask from my aparc+aseg.nii image file.
However, my mask seems to only encompass the ventricular system itself,
ignor
Hello,
I am attempting to generate a CSF mask from my aparc+aseg.nii image file.
However, my mask seems to only encompass the ventricular system itself,
ignoring any other CSF (see attached image). I attempted to make the mask
using the following MRI_binarize command with FS labels.
mri_binariz
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