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Thank you very much!
On Wed., Feb. 10, 2021, 10:05 a.m. Douglas N. Greve,
wrote:
> Use mris_anatomical_stats to create an LUT with the -c option. You can
> look in recon-all.cmd for an example. You only need to do one hemi as they
> both will be the
Use mris_anatomical_stats to create an LUT with the -c option. You can
look in recon-all.cmd for an example. You only need to do one hemi as
they both will be the same.
There are four sections of the new LUT: lh cortex, rh cortex, lh WM, and
rh WM. For each one, you replicate the LUT created
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Thanks Doug, the commands gave the expected outputs. I used the original
lh and rh BA_exvivo annotations and got the new BA+aseg.mgz and wmBA.mgz
files. Yes, please let me know how to proceed with the new LUT.
On Tue, Feb 9, 2021 at 10:47 AM
Look in the subject/scripts/recon-all.cmd file of one of your subjects.
You will find five mri_surf2volseg commands
Use the 2nd one (the one that creates aparc+aseg.mgz) as your template
and modify it to take your BA annotation and output a "BA+aseg.mgz"
Use the last one ( the one that creates
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I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve
wrote:
> which version of FS are you using?
>
> On 2/5/2021 10:02 PM, Vinny K wrote:
>
> External Email - Use Caution
> Hello,
which version of FS are you using?
On 2/5/2021 10:02 PM, Vinny K wrote:
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Hello,
I'd like to obtain white matter parcellations of the Brodmann areas.
I am not certain that the generated wmparc file from recon-all has
this type of parcellation. I was
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Hello,
I'd like to obtain white matter parcellations of the Brodmann areas. I am
not certain that the generated wmparc file from recon-all has this type of
parcellation. I was able to convert Brodmann area label files to mgz
format using
Subject: Re: [Freesurfer] White matter parcellation
The subcortical GM structures are obtained from the whole brain segmentation
(Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the
label of the closest point on cortex (Salat, Neuroimage, 2009)
On 2/1/2021 1:52 PM
The subcortical GM structures are obtained from the whole brain
segmentation (Fischl, Neuron, 2002). The segmentation of the WM is
performed by taking the label of the closest point on cortex (Salat,
Neuroimage, 2009)
On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:
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Dear FreeSurfer experts,
I need help trying to understand how the white matter gets parcellated. I have
a clinical dataset, which means that the resolution is not as research images,
but it ran without a problem. I would like to measure the volume
Hello Freesurfers,
I have a dataset of T1s and DWIs, and I have cortical ROIs defined on the T1s.
I want to use the ROIs for tractography, and therefore need them to include the
underlying white matter.
I I am aware that freesurfer can do this after running the subjects through
recon-all
[Freesurfer] white matter parcellation
Hi Laurena
yes, this is what TRACULA does. Usually it requires diffusion data, but you
might be able to run it without (which would amount to mapping the tracts
from the atlas onto your individual subject). Perhaps Anastasia can
comment?
cheers
Bruce
O
...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
Sent: 04 April 2016 15:45
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter parcellation
Hi Laurena
yes, this is what TRACULA does. Usually it requires di
Hi Laurena
yes, this is what TRACULA does. Usually it requires diffusion data, but you
might be able to run it without (which would amount to mapping the tracts
from the atlas onto your individual subject). Perhaps Anastasia can
comment?
cheers
Bruce
On Mon, 4 Apr 2016, Holleran, Laurena
Hello experts,
I wanted to know if there are any other white matter parcellation methods being developed which specifically label white matter tracts? I know that the wmparc voxel are assigned a label based on the
piece of cortex that is closest too it, however a significant portion of
Hello-
In September of 2006 there was a post in which you mentioned that white
matter parcellations were being fine-tuned but not yet ready. I'm really
hoping to take advantage of the 3000 and 4000 level labels shown in
FreeSurferColorLUT.txt, but I don't have them in my current
Hi James,
we're hoping to release it along with a bunch of other things sometime
this summer.
cheers,
Bruce
On Fri, 25 May 2007, James Porter wrote:
Hello-
In September of 2006 there was a post in which you mentioned that white
matter parcellations were being fine-tuned but not yet ready.
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